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y(eres)k(of)g(the)h(chromosomes,)d(contains)i(a)h(lar)o(ge)e(number)g (of)h(short)1974 2826 y(sequence)37 b(motifs)h(that)g(mak)o(e)g(up)f (an)h(immensely)f(rich)h(code-)1974 2921 y(book)33 b(of)i(the)g(gene)f (re)o(gulation)f(program,)k(kno)n(wn)c(as)j(the)f FK(cis-)1974 3015 y(r)o(egulatory)23 b(system)p FJ(.)43 b(It)27 b(is)g(belie)n(v)o (ed)d(that)i(this)h(re)o(gulatory)c(pro-)1974 3110 y(gram)c(determines) f(the)i(le)n(v)o(el,)f(location)g(and)g(chronology)d(of)k(gene)1974 3205 y(e)o(xpression,)25 b(which)g(signi\002cantly)-5 b(,)26 b(if)g(not)f(predominantly)-5 b(,)23 b(con-)1974 3299 y(trib)n(utes)15 b(to)h(the)f(de)n(v)o(elopmental,)e (morphological)f(and)j(beha)n(vioral)1974 3394 y(di)n(v)o(ersity)k(of)h (comple)o(x)e(or)o(ganisms)g([4].)2073 3489 y(The)e(problem)d(of)j FL(de)f(no)o(vo)g FJ(motif)g(detection)3370 3458 y FG(1)3417 3489 y FJ(has)h(been)f(widely)1974 3583 y(studied.)35 b(Numerous)22 b(algorithmic)g(approaches)f(ha)n(v)o(e)i(been)g(pro-) 1974 3678 y(posed,)31 b(most)e(of)g(which)g(use)h(probabilistic)e (generati)n(v)o(e)g(models)1974 3772 y(to)23 b(model)f(motifs)h(as)h (stochastic)f(string)f(patterns)h(randomly)e(em-)1974 3867 y(bedded)d(in)i(a)g(simple)f(background.)i(In)f(such)f(a)h (setting,)g(motif)f(de-)1974 3962 y(tection)f(can)g(be)g(formulated)e (as)j(a)g(standard)e(missing-v)n(alue)g(infer)n(-)1974 4056 y(ence)i(and)f(parameter)g(estimation)h(problem)e(\(for)h(motif)h (locations)1974 4151 y(and)32 b(position)g(weight)g(matrices,)k (respecti)n(v)o(ely\),)d(and)f(standard)1974 4246 y(methods)27 b(such)h(as)h(EM)g(and)e(Gibbs)i(sampling)e(can)h(be)g(applied.)1974 4340 y(This)j(literature)f(is)i(too)e(lar)o(ge)g(to)h(surv)o(e)o(y)e (here,)k(b)n(ut)e(some)g(rele-)1974 4435 y(v)n(ant)20 b(e)o(xamples)g(include)g(MEME)g([1)o(],)i(BioProspector)d([15)o(],)i (and)1974 4530 y(AlignA)m(CE)f([12)n(].)26 b(A)21 b(dif)n(ferent)e (frame)n(w)o(ork)g(based)h(on)g(w)o(ord)g(se)o(g-)1974 4624 y(mentation)g(and)h(dictionary)f(construction)f(w)o(as)k(proposed) c(in)j([3)o(],)1974 4719 y(which)c(pointed)g(out)h(the)g(importance)e (of)i(combinatorial)e(analysis)1974 4814 y(of)g(a)i(lar)o(ge)d(set)j (of)f(potential)e(motifs)i(jointly)-5 b(,)17 b(so)h(that)g(some)g (depen-)1974 4908 y(dencies)29 b(among)f(motifs)i(can)f(be)h(captured.) 52 b(A)30 b(similar)g(`w)o(ord-)1974 5003 y(enumeration')25 b(idea)i(also)h(appeared)d(in)j([17)n(].)47 b(Recently)-5 b(,)29 b(Gupta)1974 5097 y(and)f(Liu)h([9)o(])g(e)o(xtended)e(the)h (dictionary)f(model)h(to)h(a)g(stochastic)p 1974 5171 V 2064 5227 a FF(1)2093 5250 y FH(Not)14 b(to)g(be)f(confused)i(with)f FE(motif)g(scan)p FH(,)g(the)g(task)g(of)f(searching)j(kno)n(wn)e (motifs)1974 5325 y(based)k(on)f(gi)n(v)o(en)h(position)h(weight)f (matrices,)h(as)d(addressed)j(in)e([7)q(].)p eop %%Page: 2 2 2 1 bop -182 83 a FJ(dictionary)18 b(\(SD\))i(model)f(by)g(replacing)g (the)h(w)o(ords)f(in)i(the)f(dictio-)-182 178 y(nary)h(with)h FL(pr)l(obabilistic)f(wor)m(d)h(matrices)p FJ(,)g(allo)n(wing)f (stochastic-)-182 272 y(ity)i(of)h(motif)e(instances)i(to)g(be)f (modeled.)33 b(Man)o(y)23 b(of)g(these)h(meth-)-182 367 y(ods)j(are)g(widely)g(used)g(and)g(ha)n(v)o(e)g(been)g(successful)g (empirically)-182 462 y(for)g(motif)g(detection)f(in)i(well)g(curated)f (bacterial)g(or)g(yeast)h(gene)-182 556 y(re)o(gulatory)13 b(sequences.)22 b(Ho)n(we)n(v)o(er)m(,)15 b(generalization)f(of)h (these)h(suc-)-182 651 y(cessful)k(results)h(to)g(longer)m(,)d(more)i (comple)o(x)e(and)i(weakly)g(charac-)-182 746 y(terized)25 b(input)g(sequences)g(such)h(as)h(those)e(from)g(higher)g(eukary-)-182 840 y(otic)31 b(genomes)g(seems)h(less)h(immediate.)58 b(A)32 b(recent)f(surv)o(e)o(y)f(by)-182 935 y(Eisen)57 b([6)o(])28 b(raises)h(concerns)e(o)o(v)o(er)g(the)h(inability)g(of)g (some)g(con-)-182 1029 y(temporary)i(motif)i(models)h(to)f(incorporate) f(biological)g(kno)n(wl-)-182 1124 y(edge)17 b(of)h(global)g(motif)f (distrib)n(ution,)g(motif)h(structures)g(and)f(motif)-182 1219 y(sequence)i(composition.)-83 1313 y(Recent)33 b(w)o(ork)f(has)h (tried)f(to)h(address)f(these)h(concerns)e(from)-182 1408 y(se)n(v)o(eral)f(dif)n(ferent)g(perspecti)n(v)o(e.)58 b(F)o(or)31 b(e)o(xample,)i(some)e(authors)-182 1503 y(ha)n(v)o(e)h(proposed)e(better)i(objecti)n(v)o(e)f(functions)h(for)f (motif)i(detec-)-182 1597 y(tion,)24 b(by)f(scoring)g(motifs)g(based)h (on)f(the)h(statistical)h(signi\002cance)-182 1692 y(of)18 b(the)g(information)e(content)h([11)o(])h(and)g(considering)e (cooperati)n(v)o(e)-182 1787 y(motif)35 b(binding)f(between)i(multiple) f(transcription)f(f)o(actors)i([8)o(].)-182 1881 y(V)-9 b(an)21 b(Helden)h(et)h(al.)f([10)o(])g(recently)f(suggested)h(using)f (a)i(signature)-182 1976 y(conserv)n(ation)e(pattern)h(to)h(constrain)g (the)g(motif)g(patterns)f(and)h(in-)-182 2071 y(corporating)j(gene)h(e) o(xpression)g(data)i(from)f(microarrays.)48 b(Frith)-182 2165 y(et)22 b(al.)g([7)o(])g(used)g(an)g(HMM)g(in)g(their)g(motif)f (scanner)g(to)h(model)f(the)-182 2260 y(possible)31 b(presence)g(of)g (clustered)g(motif)g(occurrences)f(in)i(com-)-182 2354 y(ple)o(x)21 b FL(cis)p FJ(-re)o(gulatory)e(sequences.)29 b(Though)20 b(these)i(attempts)g(head)-182 2449 y(in)k(the)h(direction) e(of)i(more)f(e)o(xpressi)n(v)o(e)f(motif)h(models,)h(it)h(is)f(not) -182 2544 y(clear)i(whether)f(these)h(ideas)h(can)f(be)g(inte)o(grated) f(to)h(assemble)g(a)-182 2638 y(po)n(werful)20 b(yet)j(transparent)d (and)i(computationally)e(ef)n(\002cient)i(mo-)-182 2733 y(tif)e(detection)f(algorithm.)-83 2828 y(W)-7 b(e)42 b(are)f(interested)f(in)g(de)n(v)o(eloping)e(a)j(principled)e(general) -182 2922 y(frame)n(w)o(ork)g(for)i(motif)g(modeling,)k(which)c(is)h(e) o(xpressi)n(v)o(e)e(\(in)-182 3017 y(terms)33 b(of)g(being)g(able)g(to) h(describe)f(internal)f(structures,)k(inter)n(-)-182 3112 y(motif)28 b(relations,)i(motif)e(ab)n(undances,)g(etc.,)j(and)d (readily)g(incor)n(-)-182 3206 y(porates)33 b(prior)f(kno)n(wledge)f (from)i(e)o(xperimental)e(biology\),)k(yet)-182 3301 y(mathematically)d(and)g(algorithmically)g(transparent)g(and)h(well-) -182 3396 y(structured,)28 b(hence)f(simplifying)g(model)g (construction,)h(compu-)-182 3490 y(tation)22 b(and)g(e)o(xtension.)32 b(In)22 b(a)i(recent)e(methodological)e(paper)m(,)i(we)-182 3585 y(brie\003y)32 b(laid)h(out)f(a)h(theoretical)f(foundation)e(for)j (modular)e(mo-)-182 3680 y(tif)25 b(models)g(where)f(we)i(made)e(e)o (xplicit)h(the)g(decomposition)e(of)h(a)-182 3774 y(full)30 b(motif)g(model)g(into)g(the)h(follo)n(wing)e(tw)o(o)i(components:)44 b(the)-182 3869 y FL(global)19 b(distrib)n(ution)i(model)p FJ(,)f(which)h(models)f(the)h(frequencies)e(of)-182 3963 y(dif)n(ferent)32 b(motifs)i(and)f(the)h(dependencies)e(between)h (motif)g(oc-)-182 4058 y(currences)f(in)h(a)h(sequence;)39 b(and)33 b(the)h FL(local)f(alignment)f(model)p FJ(,)-182 4153 y(which)h(captures)g(the)i(intrinsic)e(properties)g(within)h (motifs,)j(in-)-182 4247 y(cluding)14 b(characteristic)g(position)h (weight)g(matrices)g(\(PWMs\))h(and)-182 4342 y(site)29 b(dependencies)e([22)n(].)51 b(Based)29 b(on)f(this)h(frame)n(w)o(ork,) g(we)g(e)o(x-)-182 4437 y(tended)21 b(the)i(con)m(v)o(entional)c (motif-alignment)h(model)i(into)g(a)h(v)o(ery)-182 4531 y(e)o(xpressi)n(v)o(e)14 b(hierarchical)h(Bayesian)h(Mark)o(o)o(vian)e (model,)i(called)f(a)-182 4626 y(hidden)i(Mark)o(o)o(v)g (Dirichlet-Multinomial)f(\(HMDM\))i(model,)g(for)-182 4721 y(local)29 b(alignment,)h(which)f(successfully)g(captures)f (internal)h(mo-)-182 4815 y(tif)17 b(structure)g(and)g(incorporates)e (prior)i(kno)n(wledge)e(from)h(biologi-)-182 4910 y(cally)i(kno)n(wn)e (motifs)i(using)g(a)g(structured)f(Bayesian)h(prior)f(model)-182 5005 y(for)22 b(the)h(PWMs)g(of)g(motifs.)32 b(In)23 b(the)g(current)e(paper)m(,)h(we)h(inte)o(grate)-182 5099 y(the)d(HMDM)g(model)f(into)h(a)h(general)e(frame)n(w)o(ork)f(for) i(the)g(model-)-182 5194 y(ing)25 b(of)g(motif-containing)d(biopolymer) h(sequences)i(and)g(present)-182 5288 y(a)20 b(fully)f(implemented)f (motif)i(detector)f(de)n(v)o(eloped)e(based)j(on)f(this)1974 83 y(frame)n(w)o(ork.)28 b(This)22 b(frame)n(w)o(ork)d(uses)k(the)f (HMDM)g(model)f(as)h(the)1974 178 y(local)c(alignment)f(submodel)f(and) i(uses)g(a)h(ne)n(wly)e(designed)g(HMM)1974 272 y(that)35 b(we)h(describe)e(here)h(for)f(the)i(global)e(submodel.)68 b(A)36 b FL(vari-)1974 367 y(ational)30 b(EM)h(algorithm)g FJ(is)h(de)n(v)o(eloped)c(for)j(ef)n(\002cient)f(Bayesian)1974 462 y(learning)25 b(and)g(prediction.)41 b(W)-7 b(e)27 b(call)f(our)g(frame)n(w)o(ork)e FK(LOGOS)p FJ(,)1974 556 y(for)19 b(inte)o(grated)g FK(LO)p FJ(cal)h(and)g FK(G)p FJ(l)p FK(O)p FJ(bal)g(motif)f FK(S)p FJ(equence)g(model)3863 526 y FG(2)3897 556 y FJ(.)1974 796 y FM(2)99 b(LOGOS:)50 b(A)g(Modular)g(Generati)o(v)o(e)g(Frame-)2123 907 y(w)o(ork)26 b(f)n(or)e(Motif)h(Sequences)1974 1131 y FD(2.1)90 b(Pr)n(eliminaries) 2073 1347 y FJ(Motifs)34 b(are)g(short)g(stochastic)g(string)f (patterns)g(scattered)h(in)1974 1441 y(biopolymer)14 b(sequences)i(such)g(as)h(DN)m(A)h(and)e(proteins.)22 b(The)17 b(char)n(-)1974 1536 y(acteristic)i(sequence)e(patterns)h(of)g (motifs)g(and)g(their)g(locations)g(of-)1974 1631 y(ten)i(relate)h(to)f (potentially)f(important)g(biological)g(functions)g(such)1974 1725 y(as)g(serving)e(as)h(the)g FL(cis)p FJ(-elements)g(for)f(gene)g (re)o(gulation)f(or)i(the)g(cat-)1974 1820 y(alytic)f(sites)i(for)e (protein)g(acti)n(vity)-5 b(.)23 b(Numerous)16 b(biological)g(studies) 1974 1915 y(ha)n(v)o(e)31 b(re)n(v)o(ealed)g(rich)h(architecture)f(in)h (the)g(global)f(or)o(ganization)1974 2009 y(and)h(the)g(internal)f (structures)h(of)g(motifs)g(in)g(higher)f(eukaryotic)1974 2104 y(or)o(ganisms.)51 b(T)-7 b(aking)29 b(DN)m(A)h(motifs)f(as)i(an)e (e)o(xample,)i(it)f(is)h(well)1974 2199 y(kno)n(wn)21 b(that)h(the)g FL(cis)p FJ(-re)o(gulatory)e(elements)i(often)g(occur)f (in)h(clus-)1974 2293 y(ters)h(\(referred)e(to)h(as)i FL(cis)p FJ(-modules\),)d(possibly)h(for)g(eliciting)h(syn-)1974 2388 y(er)o(gistic)d(or)g(more)f(rob)n(ust)h(re)o(gulatory)e(signals)j ([4)o(].)k(The)20 b(biophys-)1974 2482 y(ical)k(mechanisms)g(of)g(DN)m (A-protein)e(interactions)h(at)i(the)f(motif-)1974 2577 y(binding)f(sites)j(further)d(suggest)i(that)g(the)f(sites)i(within)f (the)g(DN)m(A)1974 2672 y(motifs)35 b(are)g(not)g(necessarily)f (uniformly)f(conserv)o(ed)g([21)o(,)i(20)o(].)1974 2766 y(Rather)m(,)c(the)e(conserv)n(ation)e(pattern)h(may)h(be)g(subject)g (to)g(a)h(con-)1974 2861 y(straint)25 b(imposed)f(by)h(the)g(structure) f(of)h(the)g(binding)f(protein,)g(re-)1974 2956 y(sulting)16 b(in)g(the)g(so-called)g(\223shape\224)f(bias)i(\(Figure)e(1\).)24 b(These)16 b FL(meta-)1974 3050 y(sequence)26 b(featur)m(es)g FJ(of)h(motif)f(structure)g(raise)h(signi\002cant)g(chal-)1974 3145 y(lenges)20 b(to)h(con)m(v)o(entional)c(motif-\002nding)h (algorithms,)h(which)h(pri-)1974 3240 y(marily)26 b(rely)h(on)f (simplifying)g(independence)e(assumptions)i(that)1974 3334 y(decouple)i(\(potential\))h(associations)h(among)e(sites)k (within)e(each)1974 3429 y(single)25 b(motif)f(and)h(among)e(multiple)i (instances)g(of)g(motifs.)39 b(\(F)o(or)1974 3524 y(e)o(xample,)17 b(the)h(con)m(v)o(entional)d(product)i(multinomial)f(model)i(to)g(be) 1974 3618 y(described)e(shortly)i(w)o(ould)f(assign)h(equal)f (probability)f(to)i(both)f(the)1974 3713 y(original)i(motif)h(and)f (its)i(permuted)e(v)o(ersion)g(in)h(Figure)g(1\).)2073 3807 y(In)27 b(the)f(follo)n(wing)f(paragraph,)g(we)i(introduce)d(the)j (necessary)1974 3902 y(notation)20 b(for)g(our)g(presentation.)26 b(Note)21 b(that)g(to)g(simplify)f(the)h(pre-)1974 3997 y(sentation,)i(we)g(use)g(DN)m(A)g(motifs)g(as)h(a)f(running)e(e)o (xample,)h(b)n(ut)g(it)1974 4091 y(should)27 b(be)h(clear)g(that)g(our) f(technique)g(is)i(readily)e(applicable)g(to)1974 4186 y(protein)19 b(motifs.)2073 4281 y(W)-7 b(e)33 b(denote)e(a)h(re)o (gulatory)d(DN)m(A)j(sequence)e(by)h(a)h(character)1974 4375 y(string)17 b FC(y)26 b FB(=)d(\()p FC(y)2409 4387 y FA(1)2446 4375 y FC(;)14 b(:)g(:)g(:)f(;)h(y)2671 4387 y Fz(T)2723 4375 y FB(\))24 b Fy(2)f(f)p FJ(A,T)-6 b(,C,G)o Fy(g)3223 4345 y Fz(T)3275 4375 y FJ(.)24 b(An)18 b(indicator)e(string) 1974 4470 y FC(x)30 b FJ(signals)g(the)f(locations)g(of)g(the)g(motif)g (occurrences.)50 b(F)o(ollo)n(w-)1974 4565 y(ing)31 b(biological)f(con) m(v)o(ention,)h(we)h(denote)f(the)g FL(multi-alignment)1974 4659 y FJ(of)21 b FC(M)30 b FJ(instances)21 b(of)g(a)g(motif)g(of)f (length)h FC(L)g FJ(by)f(an)h FC(M)28 b Fy(\002)19 b FC(L)i FJ(matrix)1974 4754 y Fx(A)p FJ(,)26 b(of)e(which)g(each)h FL(column)e FJ(corresponds)g(to)h(a)h FL(position)f FJ(or)g FL(site)1974 4849 y FJ(in)g(the)g(motif.)35 b(The)24 b(multi-alignment)d(of)j(all)g(instances)g(of)g(motif)p 1974 4946 788 4 v 2064 5002 a FF(2)2093 5025 y FH(Not)17 b(to)f(be)g(confused)h(with)g(\223)p FE(lo)o(go)p FH(,)-5 b(\224)18 b(a)e(graphic)h(representation)j(of)c(an)g(aligned)1974 5100 y(set)27 b(of)f(biopolymer)j(sequences)f(\002rst)f(introduced)i (by)e(T)-5 b(om)25 b(Schneider)k([19)q(])d(to)1974 5175 y(help)18 b(visualizing)i(the)e(consensus)g(and)g(the)g(entrop)o(y)h (\(or)e(\223information\224\))j(patterns)1974 5250 y(of)i(monomer)g (frequencies.)39 b(A)22 b FE(lo)o(go)h FH(is)f(not)h(a)f(motif)h (\002nding)g(algorithm,)i(b)o(ut)d(is)1974 5325 y(often)c(used)f(as)g (a)g(w)o(ay)h(to)f(present)i(motifs)e(visually)l(.)p eop %%Page: 3 3 3 2 bop -209 137 a FH(gal4:)-65 199 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 864 @rwi @setspecial %%BeginDocument: yeast_motifs/gal4.back.align.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 17 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 2 (C) numchar endstack (2) startstack 2 (G) numchar endstack (3) startstack 0.11634054809708 (C) numchar 1.51242712526204 (G) numchar endstack (4) startstack 0.108725556853473 (C) numchar 0.144967409137964 (G) numchar 0.253692965991437 (A) numchar endstack (5) startstack 0.0407206306445807 (T) numchar 0.0407206306445807 (A) numchar 0.122161891933742 (C) numchar 0.366485675801227 (G) numchar endstack (6) startstack 0.0291662301012623 (T) numchar 0.0291662301012623 (A) numchar 0.174997380607574 (G) numchar 0.174997380607574 (C) numchar endstack (7) startstack 0.0407206306445807 (T) numchar 0.0407206306445807 (C) numchar 0.122161891933742 (G) numchar 0.366485675801227 (A) numchar endstack (8) startstack 0.0525850590083181 (T) numchar 0.262925295041591 (G) numchar 0.420680472066545 (C) numchar endstack (9) startstack 0.434902227413892 (A) numchar 0.579869636551856 (T) numchar endstack (10) startstack 0.0194716661732515 (A) numchar 0.038943332346503 (T) numchar 0.0973583308662574 (C) numchar 0.116829997039509 (G) numchar endstack (11) startstack 0.0646489772562787 (G) numchar 0.193946931768836 (C) numchar 0.646489772562788 (T) numchar endstack (12) startstack 0.0316673780383698 (T) numchar 0.0316673780383698 (G) numchar 0.0475010670575546 (A) numchar 0.110835823134294 (C) numchar endstack (13) startstack 0.0194716661732515 (A) numchar 0.038943332346503 (T) numchar 0.0973583308662574 (C) numchar 0.116829997039509 (G) numchar endstack (14) startstack 0.027815911190597 (G) numchar 0.0556318223811939 (A) numchar 0.0834477335717909 (C) numchar 0.222527289524776 (T) numchar endstack (15) startstack 0.201189603059667 (G) numchar 1.207137618358 (C) numchar endstack (16) startstack 2 (C) numchar endstack (17) startstack 2 (G) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 754 63 a(gal4-)754 137 y(permute:)1017 199 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 864 @rwi @setspecial %%BeginDocument: yeast_motifs/gal4.back.permute.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 17 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.0407206306445807 (T) numchar 0.0407206306445807 (A) numchar 0.122161891933742 (C) numchar 0.366485675801227 (G) numchar endstack (2) startstack 2 (C) numchar endstack (3) startstack 2 (C) numchar endstack (4) startstack 0.108725556853473 (C) numchar 0.144967409137964 (G) numchar 0.253692965991437 (A) numchar endstack (5) startstack 0.0194716661732515 (A) numchar 0.038943332346503 (T) numchar 0.0973583308662574 (C) numchar 0.116829997039509 (G) numchar endstack (6) startstack 0.11634054809708 (C) numchar 1.51242712526204 (G) numchar endstack (7) startstack 0.0194716661732515 (A) numchar 0.038943332346503 (T) numchar 0.0973583308662574 (C) numchar 0.116829997039509 (G) numchar endstack (8) startstack 0.0407206306445807 (T) numchar 0.0407206306445807 (C) numchar 0.122161891933742 (G) numchar 0.366485675801227 (A) numchar endstack (9) startstack 0.434902227413892 (A) numchar 0.579869636551856 (T) numchar endstack (10) startstack 0.0316673780383698 (T) numchar 0.0316673780383698 (G) numchar 0.0475010670575546 (A) numchar 0.110835823134294 (C) numchar endstack (11) startstack 2 (G) numchar endstack (12) startstack 0.027815911190597 (G) numchar 0.0556318223811939 (A) numchar 0.0834477335717909 (C) numchar 0.222527289524776 (T) numchar endstack (13) startstack 2 (G) numchar endstack (14) startstack 0.0291662301012623 (T) numchar 0.0291662301012623 (A) numchar 0.174997380607574 (G) numchar 0.174997380607574 (C) numchar endstack (15) startstack 0.201189603059667 (G) numchar 1.207137618358 (C) numchar endstack (16) startstack 0.0646489772562787 (G) numchar 0.193946931768836 (C) numchar 0.646489772562788 (T) numchar endstack (17) startstack 0.0525850590083181 (T) numchar 0.262925295041591 (G) numchar 0.420680472066545 (C) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial -209 365 a(pho4:)-65 427 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 864 @rwi @setspecial %%BeginDocument: yeast_motifs/pho4.back.align.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 13 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.0639035952556319 (C) numchar 0.255614381022528 (A) numchar 0.319517976278159 (T) numchar endstack (2) startstack 0.00580988110906624 (G) numchar 0.00580988110906624 (A) numchar 0.00871482166359936 (T) numchar 0.00871482166359936 (C) numchar endstack (3) startstack 0.0429049405545331 (G) numchar 0.0429049405545331 (C) numchar 0.0858098811090662 (A) numchar 0.257429643327199 (T) numchar endstack (4) startstack 0.00580988110906628 (T) numchar 0.00580988110906628 (G) numchar 0.00871482166359942 (C) numchar 0.00871482166359942 (A) numchar endstack (5) startstack 0.0956143810225276 (C) numchar 0.191228762045055 (G) numchar 0.191228762045055 (A) numchar endstack (6) startstack 0.255614381022528 (A) numchar 1.02245752409011 (C) numchar endstack (7) startstack 0.153100440641072 (G) numchar 1.37790396576965 (A) numchar endstack (8) startstack 2 (C) numchar endstack (9) startstack 2 (G) numchar endstack (10) startstack 2 (T) numchar endstack (11) startstack 0.255614381022528 (T) numchar 1.02245752409011 (G) numchar endstack (12) startstack 0.0639035952556319 (T) numchar 0.255614381022527 (C) numchar 0.319517976278159 (G) numchar endstack (13) startstack 0.0843220350552961 (T) numchar 0.168644070110592 (A) numchar 0.590254245387072 (G) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 754 290 a(pho4-)754 365 y(permute:)1017 427 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 864 @rwi @setspecial %%BeginDocument: yeast_motifs/pho4.back.permute.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 13 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box 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3242 y Fu(\()p Ft(N)5 b Fu(\))422 3272 y Fy(g)484 3242 y FG(3)517 3272 y FJ(.)-182 3485 y FD(2.2)90 b(The)22 b(modular)g(motif)i(model)-83 3698 y FJ(W)m(ithout)i(loss)g(of)g (generality)-5 b(,)26 b(assume)g(that)g(the)g(occurrences)-182 3793 y(of)g(motifs)h(in)g(a)h(DN)m(A)f(sequence,)h(as)f(indicated)f(by) h FC(x)p FJ(,)i(are)e(go)o(v-)-182 3888 y(erned)i(by)g(a)i FK(global)e(distrib)n(ution)i(model)f FC(p)p FB(\()p FC(x)p Fy(j)p FB(\002)1366 3900 y Fz(g)1405 3888 y FC(;)14 b Fy(M)1542 3900 y Fz(g)1580 3888 y FB(\))p FJ(,)33 b(and)-182 3982 y(for)38 b(each)i(type)f(of)g(motif,)k(the)d(nucleotide)e (sequence)g(pattern)-182 4077 y(shared)21 b(by)h(all)h(its)h(instances) e(admits)h(a)f FK(local)g(alignment)h(model)-182 4172 y FC(p)p FB(\()p Fx(A)p FB(\()p FC(x;)14 b(y)s FB(\))p Fy(j)p FC(x;)g FB(\002)328 4184 y Fz(l)354 4172 y FC(;)g Fy(M)491 4184 y Fz(l)516 4172 y FB(\))p FJ(.)63 b(W)-7 b(e)33 b(further)e(assume)i(that)f(the)h(back-)-182 4266 y(ground)20 b(non-motif)h(sequences)h(are)h(modeled)f(by)g(a)i(simple)f (con-)-182 4361 y(ditional)36 b(model,)j FC(p)p FB(\()p FC(y)34 b Fy(\000)c Fx(A)p FB(\()p FC(y)s(;)14 b(x)p FB(\))p Fy(j)p FC(x;)g FB(\002)1058 4373 y Fz(bk)1129 4361 y FB(\))p FJ(,)41 b(where)36 b(the)h(back-)-182 4456 y(ground)30 b(nt-distrib)n(ution)g(parameters)h FB(\002)1054 4468 y Fz(bk)1157 4456 y FJ(are)h(assumed)g(to)h(be)-182 4550 y(estimated)26 b FL(a)g(priori)h FJ(from)e(the)h(entire)g (sequence.)43 b(The)26 b(symbols)-182 4645 y FB(\002)-117 4657 y Fz(g)-79 4645 y FJ(,)18 b FB(\002)25 4657 y Fz(l)50 4645 y FJ(,)h Fy(M)190 4657 y Fz(g)228 4645 y FJ(,)g Fy(M)368 4657 y Fz(l)411 4645 y FJ(stand)e(for)g(the)h(parameters)e (\(e.g.,)h(the)h(PWMs\))-182 4739 y(and)c(model)h(classes)i(\(e.g.,)e (a)h(product)d(multinomial)h(model\))g(in)i(the)-182 4834 y(respecti)n(v)o(e)23 b(submodels.)36 b(Thus,)25 b(the)f(lik)o(elihood)f(of)i(a)f(re)o(gulatory)-182 4929 y(sequence)19 b FC(y)k FJ(is:)p -182 5021 788 4 v -92 5077 a FF(3)-63 5100 y FH(F)o(or)14 b(simplicity)l(,)j(we)d(omit)h(the) g(superscript)h Fq(k)f FH(\(motif)g(type)g(inde)o(x\))h(of)e(v)n (ariable)-182 5175 y Fq(\022)21 b FH(and)f(the)h(superscript)g Fq(n)f FH(\(sequence)i(inde)o(x\))f(of)e(v)n(ariable)k Fq(x)c FH(and)h Fq(y)i FH(in)e(where)n(v)o(er)-182 5250 y(it)e(is)g(clear)h(from)f(the)g(conte)o(xt)i(that)f(we)f(are)h (focusing)g(on)f(a)g(generic)i(motif)e(type)h(or)-182 5325 y(a)e(generic)i(sequence.)2115 255 y FC(p)p FB(\()p FC(y)s Fy(j)p FB(\002)p FC(;)14 b Fy(M)p FB(\))23 b(=)2600 176 y Fp(X)2641 351 y Fz(x)2734 255 y FC(p)p FB(\()p FC(x)p Fy(j)p FB(\002)2943 267 y Fz(g)2982 255 y FC(;)14 b Fy(M)3119 267 y Fz(g)3157 255 y FB(\))p FC(p)p FB(\()p FC(y)s Fy(j)p FC(x;)g FB(\002)3479 267 y Fz(l)3504 255 y FC(;)g Fy(M)3641 267 y Fz(l)3666 255 y FB(\))2045 432 y(=)2133 353 y Fp(X)2174 527 y Fz(x)2266 432 y FC(p)p FB(\()p FC(x)p Fy(j)p FB(\002)2475 444 y Fz(g)2514 432 y FC(;)g Fy(M)2651 444 y Fz(g)2689 432 y FB(\))p FC(p)p FB(\()p Fx(A)p Fy(j)p FC(x;)g FB(\002)3039 444 y Fz(l)3065 432 y FC(;)g Fy(M)3202 444 y Fz(l)3227 432 y FB(\))p FC(p)p FB(\()p FC(y)n Fy(\000)-5 b Fx(A)p Fy(j)p FC(x;)14 b FB(\002)3676 444 y Fz(bk)3746 432 y FB(\))p FC(;)45 b FJ(\(1\))1974 693 y(where)37 b Fx(A)54 b Fo(,)g Fx(A)p FB(\()p FC(x;)14 b(y)s FB(\))p FJ(.)77 b(Note)37 b(that)h FB(\002)3250 705 y Fz(l)3313 693 y FJ(here)e(is)j(not)e(neces-)1974 787 y(sarily)30 b(equi)n(v)n(alent)f(to)h(the)g(PWMs)i(\()p Fr(\022)r FJ(\))e(of)g(the)g(motifs,)i(b)n(ut)f(is)g(a)1974 882 y(generic)23 b(symbol)g(for)g(parameters)g(of)h(a)g(more)f(general) g(model)g(of)1974 976 y(the)g(aligned)g(motif)g(instances.)35 b(\(E.g.,)23 b(in)h(the)g(HMDM)f(model)g(to)1974 1071 y(be)18 b(de\002ned)g(shortly)-5 b(,)17 b FB(\002)2665 1083 y Fz(l)2709 1071 y FJ(refers)h(to)h(the)f(hyperparameters)d(that)k (de-)1974 1166 y(scribe)h(a)g(distrib)n(ution)f(of)h(PWMs.\))2073 1260 y(Equation)38 b(\(1\))g(mak)o(es)g(e)o(xplicit)h(the)f(modular)g (structure)f(of)1974 1355 y(the)g FK(LOGOS)f FJ(frame)n(w)o(ork)f(for)h (generic)g(motif)g(models.)75 b(The)1974 1450 y(submodel)41 b FC(p)p FB(\()p FC(x)p Fy(j)p FB(\002)2549 1462 y Fz(g)2588 1450 y FC(;)14 b Fy(M)2725 1462 y Fz(g)2763 1450 y FB(\))43 b FJ(captures)f(properties)f(such)i(as)g(the)1974 1544 y(frequencies)33 b(of)h(dif)n(ferent)f(motifs)h(and)g(the)h (dependencies)e(be-)1974 1639 y(tween)22 b(motif)g(occurrences.)29 b(On)23 b(the)f(other)g(hand,)f(the)i(submodel)1974 1734 y FC(p)p FB(\()p Fx(A)p Fy(j)p FC(x;)14 b FB(\002)2292 1746 y Fz(l)2318 1734 y FC(;)g Fy(M)2455 1746 y Fz(l)2480 1734 y FB(\))j FJ(captures)f(the)g(intrinsic)g(properties)g(within)g (mo-)1974 1828 y(tifs)31 b(that)f(can)g(help)f(to)i(impro)o(v)o(e)d (sensiti)n(vity)h(and)h(speci\002city)g(to)1974 1923 y(genuine)24 b(motif)i(patterns.)42 b(Depending)24 b(on)i(the)g(v)n (alue)g(of)g(the)g(la-)1974 2018 y(tent)i(indicator)f FC(x)2498 2030 y Fz(t)2557 2018 y FJ(\(e.g.,)i(motif)e(or)h(not\))g(at) h(each)f(position)f FC(t)p FJ(,)k FC(y)3914 2030 y Fz(t)1974 2112 y FJ(admits)19 b(dif)n(ferent)f(probabilistic)g(distrib)n(utions,) g(such)h(as)h(a)g(partic-)1974 2207 y(ular)k(nucleotide)f(distrib)n (ution)g(inside)h(a)h(motif)f(or)g(a)h(background)1974 2301 y(distrib)n(ution.)2073 2396 y(F)o(or)d(e)o(xample,)f(the)h(con)m (v)o(entional)c FL(uniform)k(and)f(independent)1974 2491 y FJ(\(UI\))35 b(model)g(for)g(motif)h(start-positions)e(used)i(in)g (man)o(y)f(motif)1974 2585 y(\002nding)21 b(algorithms)h(is)h(an)g (instance)f(of)h(a)g(simple)f(global)g(model,)1974 2680 y(where)30 b(the)h(motif)g(instances)g(are)g(assumed)g(to)g(occur)f (indepen-)1974 2775 y(dently)17 b(with)h(uniform)e(probability)f(at)k (all)f(possible)g(locations)f(in)h(a)1974 2869 y(sequence.)27 b(So,)21 b FC(p)p FB(\()p FC(x)p FB(\))26 b(=)2726 2807 y Fp(Q)2804 2828 y Ft(M)2804 2894 y(m)p Fu(=1)2944 2869 y FC(p)p FB(\()p FC(x)3065 2881 y Fz(m)3129 2869 y FB(\))p FJ(,)c(where)e FC(p)p FB(\()p FC(x)3549 2881 y Fz(m)3614 2869 y FB(=)q FC(t)p FB(\))i 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-11648 l 2837 -11690 l 2753 -11598 l cp eoclip n 2400 -11400 m 2850 -11700 l gs col0 s gr gr % arrowhead 0 slj n 2753 -11598 m 2837 -11690 l 2720 -11648 l 2753 -11598 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 2850 -10841 m 2876 -10895 l 2742 -10961 l 2836 -10881 l 2715 -10907 l cp eoclip n 2400 -11100 m 2850 -10875 l gs col0 s gr gr % arrowhead 0 slj n 2715 -10907 m 2836 -10881 l 2742 -10961 l 2715 -10907 l cp gs 0.00 setgray ef gr col0 s /Times-Italic ff 150.00 scf sf 3225 -10725 m gs 1 -1 sc (1) col0 sh gr /Times-Italic ff 150.00 scf sf 6225 -11550 m gs 1 -1 sc (1) col0 sh gr /Times-Roman ff 180.00 scf sf 2400 -11550 m gs 1 -1 sc (1/2) col0 sh gr /Times-Roman ff 180.00 scf sf 2400 -10800 m gs 1 -1 sc (1/2) col0 sh gr /Times-Roman ff 180.00 scf sf 3675 -11775 m gs 1 -1 sc (1) col0 sh gr /Times-Roman ff 180.00 scf sf 3675 -10950 m gs 1 -1 sc (1) col0 sh gr /Times-Roman ff 180.00 scf sf 5550 -11775 m gs 1 -1 sc (1) col0 sh gr /Times-Roman ff 180.00 scf sf 5550 -10950 m gs 1 -1 sc (1) col0 sh gr % Polyline 2 slj gs clippath 7727 -11453 m 7668 -11465 l 7639 -11316 l 7692 -11428 l 7697 -11304 l cp eoclip n 7470 -11295 m 7473 -11294 l 7479 -11292 l 7488 -11289 l 7500 -11285 l 7515 -11281 l 7530 -11278 l 7546 -11276 l 7564 -11276 l 7582 -11279 l 7601 -11285 l 7620 -11295 l 7637 -11309 l 7652 -11325 l 7663 -11342 l 7671 -11359 l 7678 -11376 l 7683 -11393 l 7688 -11410 l 7695 -11445 l gs col0 s gr gr % arrowhead 0 slj n 7697 -11304 m 7692 -11428 l 7639 -11316 l 7697 -11304 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 7727 -11601 m 7670 -11617 l 7629 -11470 l 7691 -11578 l 7687 -11454 l cp eoclip n 7470 -11295 m 7472 -11296 l 7476 -11300 l 7482 -11305 l 7491 -11312 l 7502 -11322 l 7515 -11333 l 7528 -11344 l 7542 -11357 l 7556 -11371 l 7571 -11387 l 7587 -11404 l 7603 -11424 l 7620 -11445 l 7637 -11469 l 7652 -11492 l 7663 -11511 l 7671 -11528 l 7678 -11543 l 7683 -11558 l 7688 -11570 l 7695 -11595 l gs col0 s gr gr % arrowhead 0 slj n 7687 -11454 m 7691 -11578 l 7629 -11470 l 7687 -11454 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 7653 -11822 m 7597 -11845 l 7540 -11704 l 7614 -11804 l 7596 -11681 l cp eoclip n 7470 -11295 m 7471 -11297 l 7472 -11302 l 7473 -11311 l 7476 -11323 l 7480 -11338 l 7484 -11357 l 7489 -11377 l 7494 -11399 l 7500 -11422 l 7506 -11447 l 7512 -11473 l 7519 -11500 l 7527 -11530 l 7536 -11562 l 7545 -11595 l 7556 -11631 l 7565 -11663 l 7574 -11691 l 7582 -11715 l 7589 -11736 l 7595 -11754 l 7601 -11771 l 7607 -11785 l 7611 -11798 l 7620 -11820 l gs col0 s gr gr % arrowhead 0 slj n 7596 -11681 m 7614 -11804 l 7540 -11704 l 7596 -11681 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 1908 -11233 m 1952 -11274 l 1848 -11383 l 1909 -11276 l 1804 -11342 l cp eoclip n 1770 -11715 m 1769 -11713 l 1768 -11708 l 1766 -11700 l 1763 -11689 l 1759 -11675 l 1756 -11659 l 1753 -11641 l 1751 -11621 l 1751 -11600 l 1752 -11577 l 1755 -11551 l 1761 -11522 l 1770 -11490 l 1780 -11462 l 1792 -11436 l 1804 -11413 l 1817 -11391 l 1830 -11372 l 1843 -11354 l 1856 -11337 l 1868 -11321 l 1881 -11307 l 1892 -11294 l 1902 -11284 l 1920 -11265 l gs col0 s gr gr % arrowhead 0 slj n 1804 -11342 m 1909 -11276 l 1848 -11383 l 1804 -11342 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 1904 -11235 m 1953 -11270 l 1865 -11391 l 1911 -11277 l 1816 -11356 l cp eoclip n 1845 -11565 m 1844 -11563 l 1843 -11558 l 1842 -11550 l 1840 -11540 l 1838 -11527 l 1836 -11513 l 1835 -11498 l 1835 -11481 l 1837 -11462 l 1840 -11439 l 1845 -11415 l 1852 -11391 l 1860 -11368 l 1868 -11349 l 1877 -11332 l 1886 -11317 l 1894 -11302 l 1902 -11290 l 1920 -11265 l gs col0 s gr gr % arrowhead 0 slj n 1816 -11356 m 1911 -11277 l 1865 -11391 l 1816 -11356 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 1929 -11232 m 1940 -11291 l 1791 -11318 l 1904 -11267 l 1780 -11259 l cp eoclip n 1545 -11790 m 1545 -11788 l 1546 -11785 l 1548 -11778 l 1550 -11768 l 1554 -11754 l 1558 -11738 l 1563 -11719 l 1569 -11698 l 1575 -11675 l 1583 -11652 l 1591 -11627 l 1599 -11602 l 1609 -11577 l 1620 -11551 l 1631 -11525 l 1645 -11498 l 1660 -11470 l 1677 -11442 l 1695 -11415 l 1719 -11384 l 1742 -11358 l 1764 -11337 l 1784 -11320 l 1804 -11307 l 1822 -11296 l 1840 -11288 l 1857 -11281 l 1872 -11276 l 1887 -11272 l 1899 -11269 l 1920 -11265 l gs col0 s gr gr % arrowhead 0 slj n 1780 -11259 m 1904 -11267 l 1791 -11318 l 1780 -11259 l cp gs 0.00 setgray ef gr col0 s /Symbol ff 240.00 scf sf 7725 -11625 m gs 1 -1 sc (b) col0 sh gr /Times-Roman ff 135.00 scf sf 7875 -11550 m gs 1 -1 sc (1,i) col0 sh gr /Symbol ff 240.00 scf sf 1650 -11850 m gs 1 -1 sc (b) col0 sh gr /Times-Roman ff 135.00 scf sf 1800 -11775 m gs 1 -1 sc (i,1) col0 sh gr /Times-Roman ff 135.00 scf sf 7275 -10500 m gs 1 -1 sc (1,0) col0 sh gr /Times-Roman ff 180.00 scf sf 6600 -11700 m gs 1 -1 sc (1) col0 sh gr /Times-Roman ff 180.00 scf sf 6600 -11100 m gs 1 -1 sc (1) col0 sh gr % Ellipse n 4759 -7241 270 270 0 360 DrawEllipse gs col0 s gr % Polyline 2 slj gs clippath 4959 -7082 m 4918 -7038 l 5028 -6933 l 4962 -7038 l 5069 -6976 l cp eoclip n 4575 -7050 m 4573 -7048 l 4569 -7045 l 4563 -7039 l 4554 -7030 l 4542 -7018 l 4529 -7005 l 4514 -6989 l 4500 -6973 l 4486 -6956 l 4475 -6938 l 4465 -6921 l 4458 -6904 l 4456 -6887 l 4457 -6870 l 4465 -6854 l 4479 -6839 l 4500 -6825 l 4523 -6816 l 4548 -6808 l 4575 -6802 l 4602 -6798 l 4628 -6794 l 4653 -6792 l 4677 -6790 l 4699 -6789 l 4721 -6788 l 4742 -6788 l 4763 -6788 l 4783 -6788 l 4804 -6788 l 4826 -6789 l 4848 -6790 l 4872 -6792 l 4897 -6794 l 4923 -6798 l 4950 -6802 l 4977 -6808 l 5002 -6816 l 5025 -6825 l 5046 -6839 l 5060 -6854 l 5068 -6870 l 5069 -6887 l 5067 -6904 l 5060 -6921 l 5050 -6938 l 5039 -6956 l 5025 -6973 l 5011 -6989 l 4996 -7005 l 4983 -7018 l 4971 -7030 l 4950 -7050 l gs col0 s gr gr % arrowhead 0 slj n 5069 -6976 m 4962 -7038 l 5028 -6933 l 5069 -6976 l cp gs 0.00 setgray ef gr col0 s /Symbol ff 240.00 scf sf 4725 -6525 m gs 1 -1 sc (b) col0 sh gr /Times-Italic ff 330.00 scf sf 4650 -7050 m gs 1 -1 sc (b) col0 sh gr /Times-Roman ff 150.00 scf sf 4800 -7275 m gs 1 -1 sc (\(0\)) col0 sh gr /Times-Roman ff 135.00 scf sf 4875 -6450 m gs 1 -1 sc (0,0) col0 sh gr % Polyline 2 slj gs clippath 4992 -7284 m 5036 -7243 l 5140 -7352 l 5036 -7286 l 5096 -7393 l cp eoclip n 5175 -7725 m 5176 -7723 l 5177 -7718 l 5179 -7710 l 5182 -7699 l 5186 -7685 l 5189 -7669 l 5192 -7651 l 5194 -7631 l 5194 -7610 l 5193 -7587 l 5190 -7561 l 5184 -7532 l 5175 -7500 l 5165 -7472 l 5153 -7446 l 5141 -7423 l 5128 -7401 l 5115 -7382 l 5102 -7364 l 5089 -7347 l 5077 -7331 l 5064 -7317 l 5053 -7304 l 5043 -7294 l 5025 -7275 l gs col0 s gr gr % arrowhead 0 slj n 5096 -7393 m 5036 -7286 l 5140 -7352 l 5096 -7393 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 4991 -7280 m 5040 -7245 l 5128 -7366 l 5034 -7287 l 5079 -7401 l cp eoclip n 5100 -7575 m 5101 -7573 l 5102 -7568 l 5103 -7560 l 5105 -7550 l 5107 -7537 l 5109 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-7329 l 4233 -7453 l 4285 -7341 l cp eoclip n 4455 -7320 m 4452 -7319 l 4446 -7317 l 4437 -7314 l 4425 -7310 l 4410 -7306 l 4395 -7303 l 4379 -7301 l 4361 -7301 l 4343 -7304 l 4324 -7310 l 4305 -7320 l 4288 -7334 l 4273 -7350 l 4262 -7367 l 4254 -7384 l 4247 -7401 l 4242 -7418 l 4237 -7435 l 4230 -7470 l gs col0 s gr gr % arrowhead 0 slj n 4285 -7341 m 4233 -7453 l 4227 -7329 l 4285 -7341 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 4254 -7642 m 4197 -7626 l 4237 -7479 l 4234 -7603 l 4295 -7495 l cp eoclip n 4455 -7320 m 4453 -7321 l 4449 -7325 l 4443 -7330 l 4434 -7337 l 4423 -7347 l 4410 -7358 l 4397 -7369 l 4383 -7382 l 4369 -7396 l 4354 -7412 l 4338 -7429 l 4322 -7449 l 4305 -7470 l 4288 -7494 l 4273 -7517 l 4262 -7536 l 4254 -7553 l 4247 -7568 l 4242 -7583 l 4237 -7595 l 4230 -7620 l gs col0 s gr gr % arrowhead 0 slj n 4295 -7495 m 4234 -7603 l 4237 -7479 l 4295 -7495 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 4327 -7870 m 4271 -7847 l 4328 -7706 l 4311 -7829 l 4384 -7729 l cp eoclip n 4455 -7320 m 4454 -7322 l 4453 -7327 l 4452 -7336 l 4449 -7348 l 4445 -7363 l 4441 -7382 l 4436 -7402 l 4431 -7424 l 4425 -7447 l 4419 -7472 l 4413 -7498 l 4406 -7525 l 4398 -7555 l 4389 -7587 l 4380 -7620 l 4369 -7656 l 4360 -7688 l 4351 -7716 l 4343 -7740 l 4336 -7761 l 4330 -7779 l 4324 -7796 l 4318 -7810 l 4314 -7823 l 4305 -7845 l gs col0 s gr gr % arrowhead 0 slj n 4384 -7729 m 4311 -7829 l 4328 -7706 l 4384 -7729 l cp gs 0.00 setgray ef gr col0 s /Symbol ff 240.00 scf sf 5475 -7650 m gs 1 -1 sc (a) col0 sh gr /Times-Roman ff 135.00 scf sf 5625 -7575 m gs 1 -1 sc (i,0) col0 sh gr /Symbol ff 240.00 scf sf 3900 -7650 m gs 1 -1 sc (b) col0 sh gr /Times-Roman ff 135.00 scf sf 4050 -7575 m gs 1 -1 sc (0,i) col0 sh gr /Symbol ff 240.00 scf sf 6300 -7425 m gs 1 -1 sc (a) col0 sh gr /Times-Roman ff 135.00 scf sf 6450 -7350 m gs 1 -1 sc (k,0) col0 sh gr /Symbol ff 240.00 scf sf 7125 -7275 m gs 1 -1 sc (a) col0 sh gr /Times-Roman ff 135.00 scf sf 7275 -7200 m gs 1 -1 sc (1,0) col0 sh gr /Symbol ff 240.00 scf sf 2250 -7275 m gs 1 -1 sc (b) col0 sh gr /Times-Roman ff 135.00 scf sf 2400 -7200 m gs 1 -1 sc (0,1) col0 sh gr /Symbol ff 240.00 scf sf 2925 -7500 m gs 1 -1 sc (b) col0 sh gr /Times-Roman ff 135.00 scf sf 3075 -7425 m gs 1 -1 sc (0,k) col0 sh gr % Ellipse n 7159 -8891 270 270 0 360 DrawEllipse gs col0 s gr % Polyline 2 slj gs clippath 7359 -8732 m 7318 -8688 l 7428 -8583 l 7362 -8688 l 7469 -8626 l cp eoclip n 6975 -8700 m 6973 -8698 l 6969 -8695 l 6963 -8689 l 6954 -8680 l 6942 -8668 l 6929 -8655 l 6914 -8639 l 6900 -8623 l 6886 -8606 l 6875 -8588 l 6865 -8571 l 6858 -8554 l 6856 -8537 l 6857 -8520 l 6865 -8504 l 6879 -8489 l 6900 -8475 l 6923 -8466 l 6948 -8458 l 6975 -8452 l 7002 -8448 l 7028 -8444 l 7053 -8442 l 7077 -8440 l 7099 -8439 l 7121 -8438 l 7142 -8438 l 7163 -8438 l 7183 -8438 l 7204 -8438 l 7226 -8439 l 7248 -8440 l 7272 -8442 l 7297 -8444 l 7323 -8448 l 7350 -8452 l 7377 -8458 l 7402 -8466 l 7425 -8475 l 7446 -8489 l 7460 -8504 l 7468 -8520 l 7469 -8537 l 7467 -8554 l 7460 -8571 l 7450 -8588 l 7439 -8606 l 7425 -8623 l 7411 -8639 l 7396 -8655 l 7383 -8668 l 7371 -8680 l 7350 -8700 l gs col0 s gr gr % arrowhead 0 slj n 7469 -8626 m 7362 -8688 l 7428 -8583 l 7469 -8626 l cp gs 0.00 setgray ef gr col0 s /Symbol ff 240.00 scf sf 7125 -8175 m gs 1 -1 sc (b) col0 sh gr /Times-Italic ff 330.00 scf sf 7050 -8700 m gs 1 -1 sc (b) col0 sh gr /Times-Roman ff 150.00 scf sf 7200 -8925 m gs 1 -1 sc (\(k\)) col0 sh gr % Ellipse n 6135 -9315 300 300 0 360 DrawEllipse gs col0 s gr % Ellipse n 3147 -9336 300 300 0 360 DrawEllipse gs col0 s gr % Ellipse n 4350 -9300 300 300 0 360 DrawEllipse gs col0 s gr % Ellipse n 3150 -8475 300 300 0 360 DrawEllipse gs col0 s gr % Ellipse n 4950 -8475 300 300 0 360 DrawEllipse gs col0 s gr % Ellipse n 6150 -8475 300 300 0 360 DrawEllipse gs col0 s gr % Polyline gs clippath 6895 -8966 m 6929 -9016 l 6803 -9099 l 6887 -9008 l 6770 -9049 l cp eoclip n 6450 -9300 m 6900 -9000 l gs col0 s gr gr % arrowhead n 6770 -9049 m 6887 -9008 l 6803 -9099 l 6770 -9049 l cp gs 0.00 setgray ef gr col0 s % Polyline gs clippath 6929 -8758 m 6895 -8808 l 6770 -8723 l 6887 -8765 l 6803 -8673 l cp eoclip n 6900 -8775 m 6450 -8475 l gs col0 s gr gr % arrowhead n 6803 -8673 m 6887 -8765 l 6770 -8723 l 6803 -8673 l cp gs 0.00 setgray ef gr col0 s % Polyline gs clippath 4050 -9285 m 4050 -9345 l 3899 -9344 l 4019 -9314 l 3899 -9284 l cp eoclip n 3435 -9315 m 4035 -9315 l gs col0 s gr gr % arrowhead n 3899 -9284 m 4019 -9314 l 3899 -9344 l 3899 -9284 l cp gs 0.00 setgray ef gr col0 s % Polyline gs clippath 4950 -9285 m 4950 -9345 l 4799 -9344 l 4919 -9314 l 4799 -9284 l cp eoclip n 4635 -9315 m 4935 -9315 l gs col0 s gr gr % arrowhead n 4799 -9284 m 4919 -9314 l 4799 -9344 l 4799 -9284 l cp gs 0.00 setgray ef gr col0 s % Polyline gs clippath 5850 -9285 m 5850 -9345 l 5699 -9344 l 5819 -9314 l 5699 -9284 l cp eoclip n 5535 -9315 m 5835 -9315 l gs col0 s gr gr % arrowhead n 5699 -9284 m 5819 -9314 l 5699 -9344 l 5699 -9284 l cp gs 0.00 setgray ef gr col0 s % Polyline gs clippath 5865 -8445 m 5865 -8505 l 5714 -8504 l 5834 -8474 l 5714 -8444 l cp eoclip n 5250 -8475 m 5850 -8475 l gs col0 s gr gr % arrowhead n 5714 -8444 m 5834 -8474 l 5714 -8504 l 5714 -8444 l cp gs 0.00 setgray ef gr col0 s % Polyline gs clippath 4665 -8445 m 4665 -8505 l 4514 -8504 l 4634 -8474 l 4514 -8444 l cp eoclip n 4350 -8475 m 4650 -8475 l gs col0 s gr gr % arrowhead n 4514 -8444 m 4634 -8474 l 4514 -8504 l 4514 -8444 l cp gs 0.00 setgray ef gr col0 s % Polyline gs clippath 3765 -8445 m 3765 -8505 l 3614 -8504 l 3734 -8474 l 3614 -8444 l cp eoclip n 3450 -8475 m 3750 -8475 l gs col0 s gr gr % arrowhead n 3614 -8444 m 3734 -8474 l 3614 -8504 l 3614 -8444 l cp gs 0.00 setgray ef gr col0 s /Times-Roman ff 150.00 scf sf 3135 -9315 m gs 1 -1 sc (\(k\)) col0 sh gr /Times-Roman ff 150.00 scf sf 4410 -9315 m gs 1 -1 sc (\(k\)) col0 sh gr /Times-Roman ff 150.00 scf sf 6135 -9315 m gs 1 -1 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s gr % Polyline 2 slj gs clippath 2876 -9279 m 2850 -9333 l 2715 -9265 l 2836 -9292 l 2742 -9211 l cp eoclip n 2400 -9075 m 2850 -9300 l gs col0 s gr gr % arrowhead 0 slj n 2742 -9211 m 2836 -9292 l 2715 -9265 l 2742 -9211 l cp gs 0.00 setgray ef gr col0 s % Polyline 2 slj gs clippath 2845 -8441 m 2879 -8491 l 2753 -8574 l 2837 -8483 l 2720 -8524 l cp eoclip n 2400 -8775 m 2850 -8475 l gs col0 s gr gr % arrowhead 0 slj n 2720 -8524 m 2837 -8483 l 2753 -8574 l 2720 -8524 l cp gs 0.00 setgray ef gr col0 s /Times-Roman ff 180.00 scf sf 2400 -9225 m gs 1 -1 sc (1/2) col0 sh gr /Times-Roman ff 180.00 scf sf 2400 -8475 m gs 1 -1 sc (1/2) col0 sh gr /Times-Roman ff 180.00 scf sf 3675 -9375 m gs 1 -1 sc (1) col0 sh gr /Times-Roman ff 180.00 scf sf 3675 -8550 m gs 1 -1 sc (1) col0 sh gr /Times-Roman ff 180.00 scf sf 5550 -9375 m gs 1 -1 sc (1) col0 sh gr /Times-Roman ff 180.00 scf sf 5550 -8550 m gs 1 -1 sc (1) col0 sh gr % Polyline 2 slj gs clippath 7727 -9053 m 7668 -9065 l 7639 -8916 l 7692 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3132 y Fu(0)3322 3124 y Fz(;)p FA(1)3379 3112 y FC(;)14 b(:)g(:)g(:)g(;)g (\022)3603 3124 y Fz(b)3632 3132 y Fu(0)3664 3124 y Fz(;)p FA(4)3721 3112 y FB(])3744 3082 y Fs(0)3823 3112 y FJ(and)1974 3206 y FC(\022)2013 3218 y Fz(b)2042 3226 y Fu(1)2141 3206 y FB(=)61 b([)p FC(\022)2329 3218 y Fz(b)2358 3226 y Fu(1)2391 3218 y Fz(;)p FA(1)2448 3206 y FC(;)14 b(:)g(:)g(:)f(;)h (\022)2671 3218 y Fz(b)2700 3226 y Fu(1)2733 3218 y Fz(;)p FA(4)2790 3206 y FB(])2813 3176 y Fs(0)2878 3206 y FJ(for)41 b(the)g(inter)n(-)g(and)f(intra-cluster)1974 3301 y(background)46 b(nt)j(distrib)n(utions,)55 b(respecti)n(v)o(ely)48 b(\(assuming)g(all) 1974 3396 y(intra-cluster)69 b(backgrounds)e(use)k(the)f(same)h (multinomial)1974 3490 y(model\).)91 b(Thus,)48 b(gi)n(v)o(en)41 b(the)i(PWMs)h FB(\002)f FJ(of)f(motifs)h(and)f(the)1974 3585 y(background)35 b(parameters)i FB(\002)2873 3597 y Fz(bk)2999 3585 y FB(=)56 b Fy(f)p FC(\022)3201 3597 y Fz(b)3230 3605 y Fu(0)3266 3585 y FC(;)14 b(\022)3342 3597 y Fz(b)3371 3605 y Fu(1)3407 3585 y Fy(g)p FJ(,)43 b(we)c(ha)n(v)o(e)e(the)1974 3680 y(usual)27 b(joint)g(probability)e (for)h(a)h(conditional)f(HMM)h(model)f(of)h(a)1974 3774 y(motif-containing)17 b(sequence:)2152 4004 y FC(p)p FB(\()p FC(x;)d(y)s Fy(j)p FB(\002)p FC(;)g FB(\002)2544 4016 y Fz(bk)2613 4004 y FC(;)g FB(\002)2715 4016 y Fz(g)2754 4004 y FC(;)g Fy(M)2891 4016 y Fz(g)2929 4004 y FB(\))2235 4213 y(=)83 b FC(p)p FB(\()p FC(x)2504 4225 y FA(1)2542 4213 y FB(\))2618 4109 y Fz(T)2589 4134 y Fp(Y)2588 4310 y Fz(t)p FA(=2)2711 4213 y FC(p)p FB(\()p FC(x)2832 4225 y Fz(t)2861 4213 y Fy(j)p FC(x)2931 4225 y Fz(t)p Fs(\000)p FA(1)3046 4213 y FB(\))3123 4109 y Fz(T)3094 4134 y Fp(Y)3092 4310 y Fz(t)p FA(=1)3215 4213 y FC(p)p FB(\()p FC(y)3330 4225 y Fz(t)3359 4213 y Fy(j)p FC(x)3429 4225 y Fz(t)3459 4213 y FC(;)14 b FB(\002)p FC(;)g FB(\002)3663 4225 y Fz(bk)3732 4213 y FB(\))82 b FJ(\(5\))1974 4424 y(where)165 b FC(p)p FB(\()p FC(y)2458 4436 y Fz(t)2487 4424 y Fy(j)p FC(x)2557 4436 y Fz(t)2586 4424 y FC(;)14 b FB(\002)p FC(;)g FB(\002)2790 4436 y Fz(bk)2859 4424 y FB(\))84 b(=)3122 4345 y Fp(Y)3125 4523 y Fz(i)p Fs(2)p Ff(S)3283 4320 y FA(4)3247 4345 y Fp(Y)3242 4522 y Fz(j)s FA(=1)3371 4357 y Fp(\002)3406 4424 y FC(\022)3445 4436 y Fz(ij)3503 4357 y Fp(\003)3538 4374 y Fz(\016)r FA(\()p Fz(y)3630 4382 y Ft(t)3657 4374 y Fz(;j)s FA(\))p Fz(\016)r FA(\()p Fz(x)3829 4382 y Ft(t)3857 4374 y Fz(;i)p FA(\))3930 4424 y FC(:)2073 4639 y FJ(The)22 b(locations)f(of)g(all)h(motif)f (instances)h(encoded)d(in)j FC(x)h FJ(can)e(be)1974 4734 y(inferred)d(from)i(the)g(global)f(model)g(using)h(Bayes)h(rule.)p 1974 4797 788 4 v 2064 4852 a FF(7)2093 4875 y FH(When)e(no)f(strong)h (kno)n(wledge)i(about)f(modular)f(dependencies)j(is)c(a)o(v)n(ailable,) 1974 4950 y(it)j(is)g(better)i(to)e(just)h(set)f(all)h(bk-to-mt)g (transitions)i Fj(\014)3232 4958 y Fh(i;j)3306 4950 y Fj(;)13 b(i;)g(j)35 b Fk(6)p Fl(=)29 b(0)p FH(,)22 b(to)f(the)h(same) 1974 5025 y(small)17 b(constant)h(re\003ecting)h(motif)d(frequenc)o(y)l (,)i(and)f(similarly)h(for)f Fj(\014)3591 5034 y Fi(0)p Fh(;k)3694 5025 y FH(and)g Fj(\013)3855 5034 y Fh(k)q(;)p Fi(0)1974 5100 y FH(re\003ecting)27 b(cluster)f(frequenc)o(y)l(,)i(to)d (a)o(v)o(oid)g(o)o(v)o(er\002tting.)46 b(In)24 b(our)h(e)o(xperiment,)j (we)1974 5175 y(parametrize)f(our)e(HMM)f(model)h(in)f(such)h(a)f(f)o (ashion.)44 b(This)24 b(reduced)i(model)f(is)1974 5250 y(v)o(ery)18 b(similar)h(to)f(the)g(one)g(used)g(in)g(Cister)h([7],)e (b)o(ut)h(with)g(unkno)n(wn)h(PWMs)d(in)i(our)1974 5325 y(case.)p eop %%Page: 6 6 6 5 bop -83 83 a FJ(The)27 b(HMM)h(model)e(we)i(proposed)d(is)j(not)f (meant)g(to)g(capture)-182 178 y(\002ne)20 b(details)g(of)f(the)h (global)f(motif)g(dependencies,)f(because)h(with-)-182 272 y(out)j(a)g(suf)n(\002ciently)g(lar)o(ge)f(and)h (well-characterized)e(training)h(data)-182 367 y(set,)j(we)f(could)f (risk)h(o)o(v)o(er\002tting)e(to)j(hypothetical)c(structures)i(and)-182 462 y(f)o(ail)c(to)h(generalize)e(to)h(sequences)f(bearing)g(unkno)n (wn)f(\(and)h(possi-)-182 556 y(bly)f(simpler\))h(structures.)23 b(But)18 b(within)f(the)g FK(LOGOS)g FJ(frame)n(w)o(ork,)-182 651 y(if)32 b(so)h(desired,)h(we)e(can)g(easily)h(generalize)d(to)j (more)e(elaborate)-182 746 y(models,)k(such)d(as)i(one)e(that)h(models) f(higher)f(order)h(dependen-)-182 840 y(cies,)26 b(or)f(one)g(which)f (uses)i(a)f(more)f(comple)o(x)g(background)d(\(e.g.,)-182 935 y(a)g(higher)n(-order)d(Mark)o(o)o(v)h(model\))h(in)h(a)h (principled)d(w)o(ay)-5 b(.)27 b(All)22 b(that)-182 1029 y(is)j(needed)f(is)h(to)g(simply)g(e)o(xpand)e(the)h(state)i(space)f Fn(S)m FJ(,)20 b(and)k(either)-182 1124 y(train)32 b(or)g(empirically)f (parametrize)g(a)h(more)g(e)o(xpressi)n(v)o(e)f(initial)-182 1219 y(and)19 b(transition)h(model)f(in)h(the)h(global)e(HMM.)-182 1448 y FM(3)99 b(Infer)n(ence)27 b(and)f(Lear)o(ning)f(Algorithm)-182 1662 y FD(3.1)90 b(V)-8 b(ariational)22 b(Bay)o(esian)f(lear)o(ning)-83 1868 y FJ(In)15 b(order)g(to)g(do)g(Bayesian)h(estimation)f(of)g(the)g (motif)g(parameter)-182 1963 y FC(\022)r FJ(,)22 b(and)f(to)g(predict)g (the)g(locations)g(of)g(motif)g(instances)g(via)h(the)f(in-)-182 2057 y(dicator)f(sequence)f FC(x)p FJ(,)j(we)f(need)g(to)g(be)f(able)h (to)g(compute)e(the)i(pos-)-182 2152 y(terior)d(distrib)n(ution)f FC(p)p FB(\()p FC(\022)r Fy(j)p FC(y)s FB(\))p FJ(,)j(which)e(is)h (infeasible)f(in)h(closed)f(form)-182 2247 y(for)25 b(a)h(comple)o(x)e (motif)h(model)g(\(because)f(we)i(ha)n(v)o(e)f(to)h(mar)o(ginal-)-182 2341 y(ize)j(out)h FC(q)j FJ(and)c FC(x)h FJ(in)g(the)f(joint)h (posterior)e FC(p)p FB(\()p FC(\022)r(;)14 b(q)s(;)g(x)p Fy(j)p FC(y)s(;)g Fy(M)p FB(\))p FJ(\).)53 b(A)-182 2436 y(possible)28 b(approach)f(is)j(to)f(use)g(a)g(Mark)o(o)o(v)e(Chain)i (Monte)f(Carlo)-182 2531 y(\(MCMC\))17 b(method,)g(such)g(as)h(a)g (Gibbs)g(sampler)m(,)f(which)g(performs)-182 2625 y(\223asymptotically) 24 b(e)o(xact)i(inference.)-6 b(\224)41 b(Ho)n(we)n(v)o(er)m(,)26 b(concerns)e(o)o(v)o(er)-182 2720 y(lik)o(ely)18 b(slo)n(w)h(mixing)f (and)g(dif)n(\002culties)g(in)h(detecting)f(con)m(v)o(er)o(gence)-182 2815 y(moti)n(v)n(ate)31 b(us)h(to)g(use)g FL(variational)f(Bayesian)f (infer)m(ence)p FJ(,)k(which)-182 2909 y(has)21 b(a)g(more)g (deterministic)f(\003a)n(v)n(or)h(similar)g(to)g(that)g(of)g(EM)g(and)g (is)-182 3004 y(computationally)c(more)i(ef)n(\002cient.)-83 3098 y(The)37 b(v)n(ariational)e(Bayesian)i(inference)e(method)g(de)n (v)o(eloped)-182 3193 y(in)29 b([22)o(])g(for)g(the)g(HMDM)g(model)f (is)i(a)g(special)f(instance)g(of)g(the)-182 3288 y FL(g)o(ener)o (alized)c(mean)g(\002eld)h FJ(\(GMF\))g(algorithm)52 b([23)n(].)43 b(Brie\003y)-5 b(,)28 b(in)-182 3382 y(the)g(GMF)h(frame) n(w)o(ork,)f(a)h(comple)o(x)d(joint)i(distrib)n(ution)g FC(p)p FJ(,)i(such)-182 3477 y(as)22 b(the)g(joint)g(posterior)f FC(p)p FB(\()p FC(\022)r(;)14 b(q)s(;)g(x)p Fy(j)p FC(y)s(;)g Fy(M)p FB(\))p FJ(,)23 b(is)g(approximated)c(with)-182 3572 y(a)33 b(simpler)h(distrib)n(ution)e FC(Q)h FJ(de\002ned)g(by)g (the)g(product)f(of)h(inter)n(-)-182 3666 y(dependent)27 b(local)j(mar)o(ginals)e(o)o(v)o(er)h(disjoint)g(subsets)i(of)e(all)i (do-)-182 3761 y(main)23 b(v)n(ariables,)h(e.g.,)g FC(Q)p FB(\()p FC(\022)r(;)14 b(q)s(;)g(x)p FB(\))30 b(=)g FC(Q)1041 3773 y Fz(l)1066 3761 y FB(\()p FC(\022)r(;)14 b(q)s FB(\))p FC(Q)1314 3773 y Fz(g)1353 3761 y FB(\()p FC(x)p FB(\))p FJ(.)37 b(The)24 b(op-)-182 3856 y(timal)e(form)e(of)i(each)f (local)h(mar)o(ginal)e(can)h(be)h(obtained)e(via)i(min-)-182 3950 y(imizing)28 b(the)g(K)o(ullback-Leibler)e(\(KL\))i(di)n(v)o(er)o (gence)e(between)i FC(Q)-182 4045 y FJ(and)33 b FC(p)h FJ(with)g(respect)f(to)h(free)f(distrib)n(utions)g FC(Q)1275 4057 y Fz(l)1335 4045 y FJ(and)g FC(Q)1555 4057 y Fz(g)1627 4045 y FJ([23)o(].)-182 4140 y(Omitting)25 b(mathematical)h(details,)i (this)e(optimization)f(results)i(in)-182 4234 y(the)20 b(follo)n(wing)e(coupled)h(updates:)132 4415 y FC(Q)198 4427 y Fz(g)236 4415 y FB(\()p FC(x)p FB(\))84 b(=)f FC(p)p FB(\()p FC(x)p Fy(jM)823 4427 y Fz(g)862 4415 y FB(\))p FC(p)p FB(\()p FC(y)s Fy(j)p FC(x;)1130 4393 y FB(\026)1119 4415 y FC(\036)q FB(\()p FC(\022)r FB(\))p FC(;)14 b Fy(M)1411 4427 y Fz(g)1450 4415 y FB(\))208 b FJ(\(6\))74 4534 y FC(Q)140 4546 y Fz(l)165 4534 y FB(\()p FC(\022)r(;)14 b(q)s FB(\))84 b(=)f FC(p)p FB(\()p FC(q)s Fy(jM)816 4546 y Fz(l)841 4534 y FB(\))p FC(p)p FB(\()p FC(\022)r Fy(j)p FC(q)s(;)14 b(\013;)1180 4513 y FB(\026)1178 4534 y FC(h)q FB(\()p FC(y)s FB(\))p FC(;)g Fy(M)1472 4546 y Fz(l)1497 4534 y FB(\))161 b FJ(\(7\))-182 4715 y(where,)30 b FC(E)134 4727 y Fz(D)225 4715 y FJ(denotes)e(e)o (xpectation)g(with)h(respect)g(to)h(the)f(distri-)-182 4810 y(b)n(ution)22 b FC(D)r FJ(,)i(and)312 4788 y FB(\026)311 4810 y FC(h)p FB(\()p FC(y)s FB(\))29 b(=)f FC(E)650 4822 y Fz(Q)702 4830 y Ft(g)741 4810 y FB([)p FC(h)p FB(\()p FC(x;)14 b(y)s FB(\)])p FJ(,)1084 4788 y FB(\026)1073 4810 y FC(\036)p FB(\()p FC(\022)r FB(\))29 b(=)f FC(E)1410 4822 y Fz(Q)1462 4831 y Ft(l)1491 4810 y FB([ln)14 b FC(\022)r FB(])1709 4780 y FG(8)1766 4810 y FJ(,)-182 4905 y(which)h(are)g(referred)f(to)i(as)h(the)e FL(g)o(ener)o(alized)g (mean)g(\002eld)g(messa)o(g)o(es)-182 4999 y FJ(e)o(xchanged)j(between) i(submodels)f(conducting)g(probabilistic)g(in-)-182 5094 y(\003uences)g(of)h(the)h(respecti)n(v)o(e)e(submodel.)p -182 5171 788 4 v -92 5227 a FF(8)-63 5250 y Fe(ln)12 b Fq(\022)r FH(,)19 b(where)i Fe(ln\()p FO(\001)p Fe(\))e FH(is)h(a)g(componentwise)i(operation,)h(is)c(called)j(the)f FE(natur)o(al)-182 5325 y(par)o(ameterization)f FH(of)d(a)g (multinomial.)2073 83 y FJ(A)30 b(k)o(e)o(y)f(property)e(re)n(v)o (ealed)g(in)j(Eqs.)f(\(6\))f(and)h(\(7\))g(is)h(the)f(iso-)1974 178 y(morphism)36 b(of)h(their)g(right-hand)e(sides)j(to)g(those)f(of)h (the)f(Eqs.)1974 272 y(\(2\))31 b(and)g(\(5\).)60 b(Essentially)-5 b(,)34 b(the)e(v)n(ariational)e(mar)o(ginals)g FC(Q)3792 284 y Fz(g)3831 272 y FB(\()p FC(x)p FB(\))1974 367 y FJ(and)24 b FC(Q)2185 379 y Fz(l)2210 367 y FB(\()p FC(\022)r(;)14 b(q)s FB(\))26 b FJ(reco)o(v)o(er)d(e)o(xactly)h(the)h(same)f(form)g (of)h(the)f(original)1974 462 y(global)h(and)g(local)g(submodels,)h(e)o (xcept)e(that)i(the)g(motif)f(parame-)1974 556 y(ters)g FC(\022)i FJ(on)d(which)f(the)i(global)e(submodel)g(is)i(conditioned)d (are)i(re-)1974 651 y(placed)17 b(by)g(their)h(Bayesian)g(estimates)g (\(in)g(the)g(natural)f(parameter)1974 746 y(form\),)33 b(and)f(the)g(suf)n(\002cient)g(statistics)i FC(h)f FJ(propagated)c (from)i(the)1974 840 y(global)17 b(submodel)g(to)i(the)f(local)g (submodel)f(are)h(replaced)f(by)h(their)1974 935 y(posterior)e(e)o (xpectations.)23 b(This)17 b(means)h(that)g(the)f(locality)g(of)h (infer)n(-)1974 1029 y(ence)23 b(and)g(mar)o(ginalization)d(in)j(the)h (composite)e FK(LOGOS)h FJ(model)1974 1124 y(is)30 b(preserv)o(ed)d(in) j(both)e(local)h(and)g(global)f(submodels.)51 b(W)-7 b(e)30 b(can)1974 1219 y(easily)20 b(obtain)e(the)i(optimal)f (approximate)e(posterior)h(distrib)n(ution)1974 1313 y(of)26 b FC(\022)j FJ(by)c(mar)o(ginalizing)f FC(Q)2800 1325 y Fz(l)2825 1313 y FB(\()p FC(\022)r(;)14 b(q)s FB(\))27 b FJ(o)o(v)o(er)e FC(q)s FJ(,)j(and)e(that)g(of)g FC(x)h FJ(using)1974 1408 y FC(Q)2040 1420 y Fz(g)2078 1408 y FB(\()p FC(x)p FB(\))p FJ(.)f(It)18 b(can)g(be)h(further)d(pro)o (v)o(ed)g(that)j(the)f(coupled)e(updates)i(\(6\))1974 1503 y(and)28 b(\(7\))f(actually)h(optimize)g(a)h(lo)n(wer)f(bound)e (of)i(the)h(lik)o(elihood)1974 1597 y FC(p)p FB(\()p FC(y)s Fy(j)p FB(\002)p FC(;)14 b Fy(M)p FB(\))23 b FJ(and)f(are)h (guaranteed)e(to)i(con)m(v)o(er)o(ge)d(to)j(a)h(local)f(max-)1974 1692 y(imum)29 b(\(as)h(in)f(standard)g(EM\))g([13)o(].)53 b(In)29 b(the)h(follo)n(wing)d(section)1974 1787 y(we)c(summarize)e (the)i(computation)d(procedure)h(in)m(v)n(olv)o(ed)f(in)j FK(LO-)1974 1881 y(GOS)p FJ(,)17 b(which)h(we)g(call)g(a)g FL(\223variational)f(EM\224)h(algorithm)f FJ(\(VEM\),)1974 1976 y(after)j(its)h(operational)d(resemblance)h(to)h(a)h(con)m(v)o (entional)c(EM.)1974 2191 y FD(3.2)90 b(The)22 b(v)o(ariational)h(EM)f (algorithm)2073 2406 y FJ(Due)37 b(to)g(the)f(locality)g(of)g(v)n (ariational)g(Bayesian)g(inference,)1974 2500 y(we)j(can)f(perform)f (inference)g(in)i(the)f(local)h(alignment)e(model)1974 2595 y(HMDM)32 b(as)i(if)e(we)h(ha)n(v)o(e)f(\223observ)n(ations\224) 3302 2573 y FB(\026)3301 2595 y FC(h)h FJ(\(to)g(obtain)e(a)i(dis-)1974 2690 y(trib)n(ution)24 b FC(Q)2350 2702 y Fz(l)2376 2690 y FB(\()p FC(\022)r(;)14 b(q)s FB(\))27 b FJ(that)e(approximates)f(the) i(mar)o(ginalized)d(con-)1974 2784 y(ditional)g FC(p)p FB(\()p FC(\022)r(;)14 b(q)s Fy(j)p FC(y)s FB(\))p FJ(\),)25 b(and)e(in)h(the)g(global)f(HMM)h(model)f(as)i(if)f(the)1974 2879 y(position-speci\002c)17 b(multinomial)h(distrib)n(ution)f(of)i(a) g(motif)3723 2857 y FB(\026)3712 2879 y FC(\036)q FB(\()p FC(\022)r FB(\))h FJ(is)1974 2974 y(gi)n(v)o(en)25 b(\(to)i(obtain)f FC(Q)2603 2986 y Fz(g)2641 2974 y FB(\()p FC(x)p FB(\))i FJ(that)f(approximates)e FC(p)p FB(\()p FC(x)p Fy(j)p FC(y)s FB(\))p FJ(\).)45 b(There-)1974 3068 y(fore,)19 b(Bayesian)h(estimates)h(of)f(the)g(multinomial)e(parameters)h(can)1974 3163 y(be)25 b(obtained)f(via)i(\002x)o(ed-point)d(iteration)i(through) e(the)j(follo)n(wing)1974 3258 y(EM-lik)o(e)19 b(procedure:)1974 3501 y FK(V)-8 b(ariational)19 b(E)i(step:)1974 3650 y FJ(Compute)f(the)h(e)o(xpected)f(suf)n(\002cient)h(statistics,)h(the) g(count)e(matrix)1975 3723 y FB(\026)1974 3745 y FC(h)46 b FB(=)g FC(E)2240 3760 y Fz(Q)2292 3768 y Ft(g)2327 3760 y FA(\()p Fz(x)p FA(\))2421 3745 y FB([)p FC(h)p FB(])p FJ(,)36 b(via)c(inference)g(in)g(the)h(global)f(motif)g(model) 1974 3854 y(gi)n(v)o(en)2187 3832 y FB(\026)2176 3854 y FC(\036)p FB(\()p FC(\022)r FB(\))22 b FJ(and)d(sequence)h(set)g Fx(y)q FJ(:)2023 4090 y Fl(\026)2023 4109 y Fj(h)h Fl(=)2200 4016 y Fh(N)2171 4038 y Fd(X)2169 4196 y Fh(n)p Fi(=1)2297 4014 y Fh(T)2333 4022 y Ft(n)2375 4014 y FI(\000)p 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b(compare)d(three)i(v)n(ariants)-182 5041 y(of)17 b FK(LOGOS)p FJ(,)h(ordered)d(with)j(decreasing)f(model)g(e)o (xpressi)n(v)o(eness,)-182 5136 y(HMDM+HMM)f(\()p FK(LOGOS)680 5148 y Fz(hh)762 5136 y FJ(\),)i(PM+HMM)f(\()p FK(LOGOS)1544 5148 y Fz(ph)1621 5136 y FJ(\))g(and)-182 5230 y(PM+UI)41 b(\()p FK(LOGOS)437 5242 y Fz(pu)514 5230 y FJ(\),)46 b(as)c(well)g(as)g(the)f(MEME)g(and)f(Alig-)-182 5325 y(nA)m(CE)e(program)e(\(both)h(of)i(which)e(are)i(essentially)f(the)h (same)1974 83 y(as)28 b FK(LOGOS)2367 95 y Fz(pu)2473 83 y FJ(in)g(terms)g(of)f(model)g(assumptions,)i(b)n(ut)f(are)g(en-) 1974 178 y(hanced)19 b(by)i(additional)e(pattern-dri)n(v)o(en)f (submodels,)h(i.e.)27 b(gapped)1974 272 y(motifs,)20 b(and)f(a)i(more)e(sophisticated)g(implementation\).)1974 482 y FD(4.1)90 b(Lear)o(ning)21 b(the)i(HMDM)g(parameters)2073 691 y FJ(W)-7 b(e)37 b(learn)d(our)g(HMDM)i(model)e(using)g(a)i(motif)e (collection)1974 786 y(from)26 b(the)h FL(Pr)l(omoter)g(Database)e(of)i 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6 w 0 sg 3753 1448 mt 4833 1448 L 3753 258 mt 4833 258 L 3753 1448 mt 3753 258 L 4833 1448 mt 4833 258 L 3753 1448 mt 4833 1448 L 3753 1448 mt 3753 258 L 3888 1448 mt 3888 1436 L 3888 259 mt 3888 270 L 3848 1593 mt (A) s 4158 1448 mt 4158 1436 L 4158 259 mt 4158 270 L 4122 1593 mt (T) s 4428 1448 mt 4428 1436 L 4428 259 mt 4428 270 L 4382 1593 mt (G) s 4698 1448 mt 4698 1436 L 4698 259 mt 4698 270 L 4655 1593 mt (C) s 3753 1448 mt 3764 1448 L 4833 1448 mt 4821 1448 L 3652 1492 mt (0) s 3753 853 mt 3764 853 L 4833 853 mt 4821 853 L 3652 897 mt (5) s 3753 259 mt 3764 259 L 4833 259 mt 4821 259 L 3585 303 mt (10) s 3753 1448 mt 4833 1448 L 3753 258 mt 4833 258 L 3753 1448 mt 3753 258 L 4833 1448 mt 4833 258 L gs 3753 259 1081 1190 MR c np c8 0 67 216 0 0 -67 3780 1448 4 MP PP 0 sg -216 0 0 67 216 0 0 -67 3780 1448 5 MP stroke c8 0 526 216 0 0 -526 4050 1448 4 MP PP 0 sg -216 0 0 526 216 0 0 -526 4050 1448 5 MP stroke c8 0 13 216 0 0 -13 4320 1448 4 MP PP 0 sg -216 0 0 13 216 0 0 -13 4320 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1887 mt 910 1887 L 1979 1887 mt 1967 1887 L 731 1931 mt (10) s 899 3076 mt 1979 3076 L 899 1887 mt 1979 1887 L 899 3076 mt 899 1887 L 1979 3076 mt 1979 1887 L gs 899 1887 1081 1190 MR c np c8 0 451 216 0 0 -451 926 3076 4 MP PP 0 sg -216 0 0 451 216 0 0 -451 926 3076 5 MP stroke c8 0 87 216 0 0 -87 1196 3076 4 MP PP 0 sg -216 0 0 87 216 0 0 -87 1196 3076 5 MP stroke c8 0 82 216 0 0 -82 1466 3076 4 MP PP 0 sg -216 0 0 82 216 0 0 -82 1466 3076 5 MP stroke c8 0 53 216 0 0 -53 1736 3076 4 MP PP 0 sg -216 0 0 53 216 0 0 -53 1736 3076 5 MP stroke gr 1 sg 0 1189 1080 0 0 -1189 2326 3076 4 MP PP -1080 0 0 1189 1080 0 0 -1189 2326 3076 5 MP stroke 4 w DO SO 6 w 0 sg 2326 3076 mt 3406 3076 L 2326 1887 mt 3406 1887 L 2326 3076 mt 2326 1887 L 3406 3076 mt 3406 1887 L 2326 3076 mt 3406 3076 L 2326 3076 mt 2326 1887 L 2461 3076 mt 2461 3064 L 2461 1887 mt 2461 1898 L 2421 3221 mt (A) s 2731 3076 mt 2731 3064 L 2731 1887 mt 2731 1898 L 2695 3221 mt (T) s 3001 3076 mt 3001 3064 L 3001 1887 mt 3001 1898 L 2955 3221 mt (G) s 3271 3076 mt 3271 3064 L 3271 1887 mt 3271 1898 L 3228 3221 mt (C) s 2326 3076 mt 2337 3076 L 3406 3076 mt 3394 3076 L 2225 3120 mt (0) s 2326 2481 mt 2337 2481 L 3406 2481 mt 3394 2481 L 2225 2525 mt (5) s 2326 1887 mt 2337 1887 L 3406 1887 mt 3394 1887 L 2158 1931 mt (10) s 2326 3076 mt 3406 3076 L 2326 1887 mt 3406 1887 L 2326 3076 mt 2326 1887 L 3406 3076 mt 3406 1887 L gs 2326 1887 1081 1190 MR c np c8 0 95 216 0 0 -95 2353 3076 4 MP PP 0 sg -216 0 0 95 216 0 0 -95 2353 3076 5 MP stroke c8 0 101 216 0 0 -101 2623 3076 4 MP PP 0 sg -216 0 0 101 216 0 0 -101 2623 3076 5 MP stroke c8 0 61 216 0 0 -61 2893 3076 4 MP PP 0 sg -216 0 0 61 216 0 0 -61 2893 3076 5 MP stroke c8 0 215 216 0 0 -215 3163 3076 4 MP PP 0 sg -216 0 0 215 216 0 0 -215 3163 3076 5 MP stroke gr 1 sg 0 1189 1080 0 0 -1189 3753 3076 4 MP PP -1080 0 0 1189 1080 0 0 -1189 3753 3076 5 MP stroke 4 w DO SO 6 w 0 sg 3753 3076 mt 4833 3076 L 3753 1887 mt 4833 1887 L 3753 3076 mt 3753 1887 L 4833 3076 mt 4833 1887 L 3753 3076 mt 4833 3076 L 3753 3076 mt 3753 1887 L 3888 3076 mt 3888 3064 L 3888 1887 mt 3888 1898 L 3848 3221 mt (A) s 4158 3076 mt 4158 3064 L 4158 1887 mt 4158 1898 L 4122 3221 mt (T) s 4428 3076 mt 4428 3064 L 4428 1887 mt 4428 1898 L 4382 3221 mt (G) s 4698 3076 mt 4698 3064 L 4698 1887 mt 4698 1898 L 4655 3221 mt (C) s 3753 3076 mt 3764 3076 L 4833 3076 mt 4821 3076 L 3652 3120 mt (0) s 3753 2481 mt 3764 2481 L 4833 2481 mt 4821 2481 L 3652 2525 mt (5) s 3753 1887 mt 3764 1887 L 4833 1887 mt 4821 1887 L 3585 1931 mt (10) s 3753 3076 mt 4833 3076 L 3753 1887 mt 4833 1887 L 3753 3076 mt 3753 1887 L 4833 3076 mt 4833 1887 L gs 3753 1887 1081 1190 MR c np c8 0 179 216 0 0 -179 3780 3076 4 MP PP 0 sg -216 0 0 179 216 0 0 -179 3780 3076 5 MP stroke c8 0 238 216 0 0 -238 4050 3076 4 MP PP 0 sg -216 0 0 238 216 0 0 -238 4050 3076 5 MP stroke c8 0 117 216 0 0 -117 4320 3076 4 MP PP 0 sg -216 0 0 117 216 0 0 -117 4320 3076 5 MP stroke c8 0 136 216 0 0 -136 4590 3076 4 MP 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216 0 0 -150 5207 3076 5 MP stroke c8 0 143 216 0 0 -143 5477 3076 4 MP PP 0 sg -216 0 0 143 216 0 0 -143 5477 3076 5 MP stroke c8 0 176 216 0 0 -176 5747 3076 4 MP PP 0 sg -216 0 0 176 216 0 0 -176 5747 3076 5 MP stroke c8 0 238 216 0 0 -238 6017 3076 4 MP PP 0 sg -216 0 0 238 216 0 0 -238 6017 3076 5 MP stroke gr %%IncludeResource: font Helvetica /Helvetica /ISOLatin1Encoding 192 FMSR 601 2866 mt -90 rotate (Posterior Dirichlet parameters ) s 90 rotate end eplot %%EndObject epage end showpage %%Trailer %%EOF %%EndDocument @endspecial 1403 w @beginspecial 84 @llx 476 @lly 187 @urx 594 @ury 648 @rwi @setspecial %%BeginDocument: newplots/fig_trans.eps %!PS-Adobe-2.0 EPSF-1.2 %%Creator: MATLAB, The Mathworks, Inc. %%Title: /.automount/coeus/vol/vol0/eecs/epxing/work/Projects/GeneNet/results/fig_trans.eps %%CreationDate: 06/25/2002 19:42:48 %%DocumentNeededFonts: Helvetica %%DocumentProcessColors: Cyan Magenta Yellow Black %%Extensions: CMYK %%Pages: 1 %%BoundingBox: 84 476 187 594 %%EndComments %%BeginProlog % MathWorks dictionary /MathWorks 160 dict begin % definition operators /bdef {bind def} bind def /ldef {load def} bind def /xdef {exch def} bdef /xstore {exch store} bdef % operator abbreviations /c /clip ldef /cc /concat ldef /cp /closepath ldef /gr /grestore ldef /gs /gsave ldef /mt /moveto ldef /np /newpath ldef /cm /currentmatrix ldef /sm /setmatrix ldef /rm /rmoveto ldef /rl /rlineto ldef /s /show ldef /sc {setcmykcolor} bdef /sr /setrgbcolor ldef /sg /setgray ldef /w /setlinewidth ldef /j /setlinejoin ldef /cap /setlinecap ldef /rc {rectclip} bdef /rf {rectfill} bdef % page state control /pgsv () def /bpage {/pgsv save def} bdef /epage {pgsv restore} bdef /bplot /gsave ldef /eplot {stroke grestore} bdef % orientation switch /portraitMode 0 def /landscapeMode 1 def /rotateMode 2 def % coordinate system mappings /dpi2point 0 def % font control /FontSize 0 def /FMS {/FontSize xstore findfont [FontSize 0 0 FontSize neg 0 0] makefont setfont} bdef /reencode {exch dup where {pop load} {pop StandardEncoding} ifelse exch dup 3 1 roll findfont dup length dict begin { 1 index /FID ne {def}{pop pop} ifelse } forall /Encoding exch def currentdict end definefont pop} bdef /isroman {findfont /CharStrings get /Agrave known} bdef /FMSR {3 1 roll 1 index dup isroman {reencode} {pop pop} ifelse exch FMS} bdef /csm {1 dpi2point div -1 dpi2point div scale neg translate dup landscapeMode eq {pop -90 rotate} {rotateMode eq {90 rotate} if} ifelse} bdef % line types: solid, dotted, dashed, dotdash /SO { [] 0 setdash } bdef /DO { [.5 dpi2point mul 4 dpi2point mul] 0 setdash } bdef /DA { [6 dpi2point mul] 0 setdash } bdef /DD { [.5 dpi2point mul 4 dpi2point mul 6 dpi2point mul 4 dpi2point mul] 0 setdash } bdef % macros for lines and objects /L {lineto stroke} bdef /MP {3 1 roll moveto 1 sub {rlineto} repeat} bdef /AP {{rlineto} repeat} bdef /PDlw -1 def /W {/PDlw currentlinewidth def setlinewidth} def /PP {closepath eofill} bdef /DP {closepath stroke} bdef /MR {4 -2 roll moveto dup 0 exch rlineto exch 0 rlineto neg 0 exch rlineto closepath} bdef /FR {MR stroke} bdef /PR {MR fill} bdef /L1i {{currentfile picstr readhexstring pop} image} bdef /tMatrix matrix def /MakeOval {newpath tMatrix currentmatrix pop translate scale 0 0 1 0 360 arc tMatrix setmatrix} bdef /FO {MakeOval stroke} bdef /PO {MakeOval fill} bdef /PD {currentlinewidth 2 div 0 360 arc fill PDlw -1 eq not {PDlw w /PDlw -1 def} if} def /FA {newpath tMatrix currentmatrix pop translate scale 0 0 1 5 -2 roll arc tMatrix setmatrix stroke} bdef /PA {newpath tMatrix currentmatrix pop translate 0 0 moveto scale 0 0 1 5 -2 roll arc closepath tMatrix setmatrix fill} bdef /FAn {newpath tMatrix currentmatrix pop translate scale 0 0 1 5 -2 roll arcn tMatrix setmatrix stroke} bdef /PAn {newpath tMatrix currentmatrix pop translate 0 0 moveto scale 0 0 1 5 -2 roll arcn closepath tMatrix setmatrix fill} bdef /vradius 0 def /hradius 0 def /lry 0 def /lrx 0 def /uly 0 def /ulx 0 def /rad 0 def /MRR {/vradius xdef /hradius xdef /lry xdef /lrx xdef /uly xdef /ulx xdef newpath tMatrix currentmatrix pop ulx hradius add uly vradius add translate hradius vradius scale 0 0 1 180 270 arc tMatrix setmatrix lrx hradius sub uly vradius add translate hradius vradius scale 0 0 1 270 360 arc tMatrix setmatrix lrx hradius sub lry vradius sub translate hradius vradius scale 0 0 1 0 90 arc tMatrix setmatrix ulx hradius add lry vradius sub translate hradius vradius scale 0 0 1 90 180 arc tMatrix setmatrix closepath} bdef /FRR {MRR stroke } bdef /PRR {MRR fill } bdef /MlrRR {/lry xdef /lrx xdef /uly xdef /ulx xdef /rad lry uly sub 2 div def newpath tMatrix currentmatrix pop ulx rad add uly rad add translate rad rad scale 0 0 1 90 270 arc tMatrix setmatrix lrx rad sub lry rad sub translate rad rad scale 0 0 1 270 90 arc tMatrix setmatrix closepath} bdef /FlrRR {MlrRR stroke } bdef /PlrRR {MlrRR fill } bdef /MtbRR {/lry xdef /lrx xdef /uly xdef /ulx xdef /rad lrx ulx sub 2 div def newpath tMatrix currentmatrix pop ulx rad add uly rad add translate rad rad scale 0 0 1 180 360 arc tMatrix setmatrix lrx rad sub lry rad sub translate rad rad scale 0 0 1 0 180 arc tMatrix setmatrix closepath} bdef /FtbRR {MtbRR stroke } bdef /PtbRR {MtbRR fill } bdef /stri 6 array def /dtri 6 array def /smat 6 array def /dmat 6 array def /tmat1 6 array def /tmat2 6 array def /dif 3 array def /asub {/ind2 exch def /ind1 exch def dup dup ind1 get exch ind2 get sub exch } bdef /tri_to_matrix { 2 0 asub 3 1 asub 4 0 asub 5 1 asub dup 0 get exch 1 get 7 -1 roll astore } bdef /compute_transform { dmat dtri tri_to_matrix tmat1 invertmatrix smat stri tri_to_matrix tmat2 concatmatrix } bdef /ds {stri astore pop} bdef /dt {dtri astore pop} bdef /db {2 copy /cols xdef /rows xdef mul dup 3 mul string currentfile exch readhexstring pop dup 0 3 index getinterval /rbmap xdef dup 2 index dup getinterval /gbmap xdef 1 index dup 2 mul exch getinterval /bbmap xdef pop pop}bdef /it {gs np dtri aload pop moveto lineto lineto cp c cols rows 8 compute_transform rbmap gbmap bbmap true 3 colorimage gr}bdef /il {newpath moveto lineto stroke}bdef currentdict end def %%EndProlog %%BeginSetup MathWorks begin 0 cap end %%EndSetup %%Page: 1 1 %%BeginPageSetup %%PageBoundingBox: 84 476 187 594 MathWorks begin bpage %%EndPageSetup %%BeginObject: obj1 bplot /dpi2point 12 def portraitMode 0216 7344 csm 798 211 1231 1410 MR c np 92 dict begin %Colortable dictionary /c0 { 0 0 0 sr} bdef /c1 { 1 1 1 sr} bdef /c2 { 1 0 0 sr} bdef /c3 { 0 1 0 sr} bdef /c4 { 0 0 1 sr} bdef /c5 { 1 1 0 sr} bdef /c6 { 1 0 1 sr} bdef /c7 { 0 1 1 sr} bdef c0 1 j 1 sg 0 0 6917 3457 PR 6 w 0 -1189 1080 0 0 1189 899 259 4 MP PP -1080 0 0 -1189 1080 0 0 1189 899 259 5 MP stroke gs 899 259 1081 1190 MR c np gs np 899 259 mt 0 1189 rl 1080 0 rl 0 -1189 rl cp c np [1080 0 0 1189 899 259] cc /picstr 24 string def 8 8 8 [8.000000 0 0 8.000000 0 0] {currentfile picstr readhexstring pop} false 3 colorimage 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y(the)g(HMM)h(global)f(model,)i(can)e(yield)h(substantially)f (impro)o(v)o(ed)-182 4582 y(performance.)40 b(Our)27 b(results)f(are)h(reasonably)d(rob)n(ust)i(under)f(dif-)-182 4676 y(ferent)j(choices)g(of)g(the)h(global)f(HMM)h(parameters,)h(b)n (ut)e(due)h(to)-182 4771 y(space)20 b(limitations,)f(we)i(omit)f (details.)-182 4985 y FK(4.2.2)81 b(Simultaneous)20 b(detection)g(of)g (multiple)h(motifs)-182 5136 y FJ(Detecting)e(multiple)g(motifs)h (simultaneously)e(is)j(ar)o(guably)d(a)i(bet-)-182 5230 y(ter)j(strate)o(gy)g(than)h(detecting)e(one)h(at)i(a)f(time)g(follo)n (wed)e(by)h(delet-)-182 5325 y(ing)i(or)g(masking)f(the)i(detected)e (motifs,)j(especially)e(when)f(motif)1974 83 y(concentrations)d(are)j (high,)f(because)g(the)g(latter)h(strate)o(gy)f(mistak-)1974 178 y(enly)i(treats)i(the)f(other)f(motifs)h(as)h(background,)c (causing)i(poten-)1974 272 y(tially)f(suboptimal)f(estimation)h(of)g (both)g(motif)g(and)g(background)1974 367 y(parameters.)54 b(The)30 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b(the)h(VEM\))f(posterior)f(e)o(xpectation)g(of)h FC(x)p FJ(.)66 b(Note)33 b(that)h(with)1974 1408 y(a)c(HMDM)h(local)f (model,)i FK(LOGOS)3089 1420 y Fz(hh)3202 1408 y FJ(e)o(xhibits)d (better)h(perfor)n(-)1974 1503 y(mance.)23 b(In)18 b(the)g(lo)n(wer)g (panels,)g(we)g(sho)n(w)g(the)g(best)g(FP-FN)h(results)1974 1597 y(in)j(the)h(top)f(three)g(predictions)f(made)h(by)g FK(LOGOS)g FJ(\(note)g(the)g(`)p FC(k)s FJ(-)1974 1692 y(at-a-time')c(prediction)f(yields)i(a)g(total)h(of)e FB(3)p FC(k)k FJ(possibly)d(redundant)1974 1787 y(motif)30 b(patterns\).)55 b(This)30 b(is)i(close)e(to)h(the)f(stochastic)h (dictionary)1974 1881 y(scenario)24 b(where)f(the)i(predicted)e(motif)h (is)h(to)g(be)f(identi\002ed)g(from)1974 1976 y(optimal)g(dictionary)g (of)h(patterns)g(resulting)f(from)g(the)i(motif)f(de-)1974 2071 y(tection)i(program)e([9)o(].)47 b(It)28 b(is)h(e)o(xpected)c (that)j(a)g(human)e(observ)o(er)1974 2165 y(could)18 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(is)k(permissible,)f(and)f(as)i(a)f(result,)h(we)1974 4105 y(do)j(not)g(ha)n(v)o(e)f(to)i(kno)n(w)e(the)h(e)o(xact)g(length)f (of)h(the)g(motif.)58 b(This)1974 4200 y(is)39 b(another)e(appealing)f (feature)h(of)h FK(LOGOS)p FJ(,)g(which)f(e)o(xtends)1974 4294 y(its)29 b(\003e)o(xibility)-5 b(.)48 b(As)28 b(sho)n(wn)g(in)g(T) -7 b(able)28 b(3,)i(e)n(v)o(en)d(in)h(simultaneous)1974 4389 y(multiple)j(motif)g(detection,)i(with)e(improperly)e(speci\002ed) j(motif)1974 4484 y(lengths,)g(HMDM+HMM)d(performs)g(nearly)g(as)i (well)g(as)g(when)1974 4578 y(motif)17 b(lengths)h(are)g(precisely)f (speci\002ed,)h(whereas)f(PM+HMM)h(is)1974 4673 y(not)i(as)h(good.)1974 4876 y FD(4.3)90 b(P)n(erf)n(ormance)20 b(on)i(r)n(eal)h(genomic)e (sequence)f(data)1974 5079 y FK(4.3.1)81 b(Motif)20 b(detection)f(in)i (y)o(east)f(pr)o(omoter)f(r)o(egions)1974 5230 y FJ(In)h(this)h (section)f(we)h(report)e(a)i(performance)c(comparison)i(of)h FK(LO-)1974 5325 y(GOS)34 b FJ(\(HMM+HMDM\))e(with)i(tw)o(o)h(popular)d (motif)h(detection)p eop %%Page: 9 9 9 8 bop -83 81 a Fw(T)-7 b(ab)o(le)33 b(3.)g FH(Simultaneous)25 b(detection)h(of)d(three)h(motifs,)g(with)g(lengths)-83 155 y(improperly)29 b(speci\002ed)f(\(18,)h(22,)f(20)f(bp,)i(respecti)n (v)o(ely)l(,)j(instead)c(of)f(the)-83 230 y(actual)19 b(13,)e(17,)g(11)g(bp\).)p 110 339 1349 4 v 108 402 4 64 v 397 402 V 108 418 V 397 418 V 524 399 a Fb(LOGOS)731 408 y Ft(hh)p 927 418 V 1056 399 a Fb(LOGOS)1262 408 y Ft(ph)p 1457 418 V 108 481 V 397 481 V 448 463 a FG(FP)201 b(FN)p 927 481 V 191 w(FP)g(FN)p 1457 481 V 110 485 1349 4 v 108 548 4 64 v 397 548 V 108 564 V 160 545 a(abf1)p 397 564 V 185 w(0.7295)105 b(0.6667)p 927 564 V 105 w(0.8021)g(0.7680)p 1457 564 V 108 627 V 160 608 a(gal4)p 397 627 V 188 w(0.1167)g(0.2042)p 927 627 V 105 w(0.2357)g(0.1325)p 1457 627 V 108 690 V 160 671 a(mig1)p 397 690 V 169 w(0.4183)g(0.2128)p 927 690 V 105 w(0.8150)g(0.8381)p 1457 690 V 110 693 1349 4 v 108 756 4 64 v 397 756 V 108 772 V 160 753 a(abf1)p 397 772 V 185 w(0.3310)g(0.2804)p 927 772 V 105 w(0.5742)g(0.4821)p 1457 772 V 108 835 V 160 816 a(gal4)p 397 835 V 188 w(0.0955)g(0.1222)p 927 835 V 105 w(0.1882)g(0.1250)p 1457 835 V 108 898 V 160 879 a(mig1)p 397 898 V 169 w(0.2124)g(0.1327)p 927 898 V 105 w(0.3218)g(0.1623)p 1457 898 V 110 902 1349 4 v -182 1069 a FJ(programs,)19 b(MEME)i(and)f(AlignA)m(CE,)g(on)h (12)g(yeast)g(genomic)f(se-)-182 1164 y(quence)c(sets)i(gathered)d (from)i(the)g(SCPD)h(database)f(\(the)g(selection)-182 1259 y(is)30 b(based)f(on)g(ha)n(ving)g(at)h(least)g(a)g(total)g(of)f (5)g(motif)g(instances)h(in)-182 1353 y(all)22 b(sequences)e(and)h(the) h(motif)e(being)h(independent)e(of)i(our)g(train-)-182 1448 y(ing)j(set\).)39 b(Each)24 b(sequence)g(set)h(consists)h(of)e (multiple)g(yeast)h(pro-)-182 1542 y(moter)30 b(re)o(gions)g(each)h (about)f(500)h(bp)g(long)f(and)h(containing)e(on)-182 1637 y(both)c(strands)h(an)g(unkno)n(wn)e(number)h(of)h(occurrences)e (of)i(a)h(pre-)-182 1732 y(dominant)i(motif)i(\(b)n(ut)g(also)g (possibly)g(other)f(minor)h(motifs\))f(as)-182 1826 y(speci\002ed)i(by) f(the)i(name)e(of)h(the)h(dataset)f(\(T)-7 b(able)32 b(4,)j(where)d(the)-182 1921 y(rightmost)d(column)h(gi)n(v)o(es)g(the)h (number)e(of)i(sequences)f(in)h(each)-182 2016 y(dataset\).)67 b(Note)34 b(that)h(both)e(the)i(relati)n(v)o(ely)e(lar)o(ge)g(sizes)j (of)e(the)-182 2110 y(input)26 b(sequences)h(and)g(the)h(possible)f (presence)g(of)g(motifs)h(other)-182 2205 y(than)e(what)g(has)h(been)f (annotated)f(mak)o(e)h(the)h(motif)f(\002nding)g(task)-182 2300 y(signi\002cantly)20 b(more)h(dif)n(\002cult)g(than)g(a)h (semi-realistic)f(test)i(data)e(or)-182 2394 y(a)28 b(small,)h(well)g (curated)d(real)i(test)g(data.)47 b(W)-7 b(e)29 b(use)f(the)g(follo)n (wing)-182 2489 y(command)j(to)i(run)f(MEME:)h(\223)g(meme)g($e\002le)g (-p)g(2)g(-dna)f(-mod)-182 2584 y(tcm)h(-re)n(vcomp)e(-nmotifs)h(1)h (\224.)65 b(In)33 b(practice,)i(this)f(means)f(that)-182 2678 y(we)23 b(search)g(for)f(a)i(DN)m(A)g(sequence)e(on)g(both)h (strands)g(for)f(at)i(most)-182 2773 y(one)18 b(motif,)h(which)g(can)g (occur)f(zero)h(or)g(more)f(times)i(in)g(an)o(y)e(gi)n(v)o(en)-182 2867 y(sequence.)33 b(AlignA)m(CE)22 b(is)j(run)d(with)i(def)o(ault)e (command-line)f(ar)n(-)-182 2962 y(guments)e(nearly)h(identical)g(to)h (those)f(for)g(MEME,)g(with)h(the)g(only)-182 3057 y(dif)n(ference)15 b(that)i(AlignA)m(CE)g(can)g(return)f(multiple)h(predicted)f(mo-)-182 3151 y(tifs)31 b(\(of)g(which)g(we)g(select)h(the)f(best)g(match)g (from)f(the)h(top)g(\002)n(v)o(e)-182 3246 y(MAP)21 b(predictions\).)j FK(LOGOS)c FJ(is)i(set)f(in)g(the)g(multiple-detection)-182 3341 y(mode)28 b(and)h(is)h(used)f(to)g(mak)o(e)g(tw)o(o)h(motif)e (predictions)g(simulta-)-182 3435 y(neously)-5 b(.)38 b(As)26 b(sho)n(wn)f(in)g(T)-7 b(able)25 b(4,)i(for)d(this)i(non-tri)n (vial)e FL(de)h(no)o(vo)-182 3530 y FJ(motif)31 b(detection)h(task,)j FK(LOGOS)d FJ(outperforms)e(the)i(other)g(tw)o(o)-182 3625 y(programs)18 b(by)i(a)g(signi\002cant)g(mar)o(gin.)-83 3794 y Fw(T)-7 b(ab)o(le)30 b(4.)g FH(Comparison)22 b(of)f(motif)h (detectors)h(on)e(yeast)h(promoter)g(se-)-83 3869 y(quences.)p -182 3978 2009 4 v -184 4041 4 64 v 57 4041 V -184 4057 V -133 4038 a FG(set)p 57 4057 V 289 w Fb(LOGOS)p 587 4057 V 340 w FG(MEME)p 1117 4057 V 318 w(AlignA)n(CE)p 1647 4057 V 191 w(seq)p 1824 4057 V -184 4120 V -133 4101 a(name)p 57 4120 V 116 w(FP)201 b(FN)p 587 4120 V 191 w(FP)g(FN)p 1117 4120 V 191 w(FP)g(FN)p 1647 4120 V 191 w(no.)p 1824 4120 V -182 4123 2009 4 v -184 4186 4 64 v 57 4186 V -184 4202 V -133 4183 a(abf1)p 57 4202 V 139 w(0.7949)105 b(0.6522)p 587 4202 V 105 w(1.0000)g(1.0000)p 1117 4202 V 105 w Fb(0.5294)g(0.6087)p 1647 4202 V 105 w FG(20)p 1824 4202 V -184 4265 V -133 4246 a(csre)p 57 4265 V 148 w Fb(0.4444)g(0.1667)p 587 4265 V 105 w FG(0.7778)g(0.5000)p 1117 4265 V 105 w(0.8000)g(0.5000)p 1647 4265 V 105 w(4)p 1824 4265 V -184 4328 V -133 4309 a(gal4)p 57 4328 V 142 w Fb(0.1333)g(0.0714)p 587 4328 V 105 w FG(0.1667)g(0.2857)p 1117 4328 V 105 w(0.3333)g(0.1429)p 1647 4328 V 105 w(6)p 1824 4328 V -184 4391 V -133 4372 a(gcn4)p 57 4391 V 129 w Fb(0.3529)g(0.1852)p 587 4391 V 105 w FG(1.0000)g(1.0000)p 1117 4391 V 105 w(0.3333)g(0.5556)p 1647 4391 V 105 w(9)p 1824 4391 V -184 4454 V -133 4436 a(gcr1)p 57 4454 V 139 w Fb(0.2859)g(0.6154)p 587 4454 V 105 w FG(1.0000)g(1.0000)p 1117 4454 V 105 w(0.4545)g(0.4615)p 1647 4454 V 105 w(6)p 1824 4454 V -184 4518 V -133 4499 a(hstf)p 57 4518 V 155 w(0.8571)g(0.5556)p 587 4518 V 105 w Fb(0.6000)g(0.5556)p 1117 4518 V 105 w FG(0.8500)g(0.6667)p 1647 4518 V 105 w(6)p 1824 4518 V -184 4581 V -133 4562 a(mat)p 57 4581 V 155 w Fb(0.4194)g(0)p 587 4581 V 236 w FG(0.3750)g(0.5625)p 1117 4581 V 105 w(0.2500)g(0.2500)p 1647 4581 V 105 w(7)p 1824 4581 V -184 4644 V -133 4625 a(mcb)p 57 4644 V 142 w(0.4706)g(0.2500)p 587 4644 V 105 w(0.2000)g(0.3333)p 1117 4644 V 105 w Fb(0.2500)g(0.2500)p 1647 4644 V 105 w FG(6)p 1824 4644 V -184 4707 V -133 4688 a(mig1)p 57 4707 V 123 w Fb(0.8077)g(0.2857)p 587 4707 V 105 w FG(1.0000)g(1.0000)p 1117 4707 V 105 w(0.8333)g(0.7857)p 1647 4707 V 105 w(22)p 1824 4707 V -184 4770 V -133 4751 a(pho2)p 57 4770 V 126 w Fb(0.9024)g(0.5000)p 587 4770 V 105 w FG(1.0000)g(1.0000)p 1117 4770 V 105 w(1.0000)g(1.0000)p 1647 4770 V 105 w(3)p 1824 4770 V -184 4833 V -133 4814 a(swi5)p 57 4833 V 132 w Fb(0.7647)g(0.5000)p 587 4833 V 105 w FG(1.0000)g(1.0000)p 1117 4833 V 105 w(0.9412)g(0.7500)p 1647 4833 V 105 w(2)p 1824 4833 V -184 4896 V -133 4877 a(uash)p 57 4896 V 135 w Fb(0.8250)g(0.6818)p 587 4896 V 105 w FG(1.0000)g(1.0000)p 1117 4896 V 105 w(0.9231)g(0.9545)p 1647 4896 V 105 w(18)p 1824 4896 V -182 4899 2009 4 v -182 5080 a FK(4.3.2)81 b(Motif)20 b(detection)f(in)i(Dr)o(osophila)f (r)o(egulatory)d(DN)n(As)-182 5230 y FJ(In)g(this)h(section)f(we)h (report)e(on)h(a)h(preliminary)e FL(de)h(no)o(vo)g FJ(motif)g(dis-)-182 5325 y(co)o(v)o(ery)c(analysis)i(of)g(the)h(re)o(gulatory)d(re)o(gions) h(of)h(the)g(9)g(Drosophila)1974 83 y(genes)24 b(in)m(v)n(olv)o(ed)f (in)i(body)e(se)o(gmentation.)37 b(The)24 b(input)g(data)h(con-)1974 178 y(sists)30 b(of)d(19)h(DN)m(A)g(sequences)g(ranging)e(from)h(512)g (to)h(5218)f(bp,)1974 272 y(as)h(described)f(in)h([2)o(].)48 b(Biologically)27 b(identi\002ed)g(motifs)g(include)1974 367 y FL(bcd)p FJ(,)h FL(cad)p FJ(,)f FL(hb)p FJ(,)h FL(kni)f FJ(and)g FL(kr)p FJ(.)45 b(F)o(or)27 b(comparison,)f(we)h(pro) o(vide)e(the)1974 462 y(PWMs)30 b(postulated)e(by)h(Berman)f(et)h(al.) 52 b(for)29 b(these)g(\002)n(v)o(e)g(motifs,)1974 556 y(which)16 b(were)h(used)g(in)g(their)f FL(motif)h(scan)g FJ(analysis)g(\(Figure)f(5\).)24 b(The)1974 651 y(sources)30 b(of)h(all)h(PWMs)g(are)f(biologically)e(identi\002ed)h(sequence)1974 746 y(se)o(gments)22 b(from)g(the)h(literature)f(\(which)g(are)h (unaligned,)e(ranging)1974 840 y(from)h(5)h(to)g(93)f(instances)h(per)g (motif,)g(and)f(about)g FB(20)27 b Fy(\030)h FB(40)23 b FJ(bases)1974 935 y(in)e(length\).)k(The)20 b(PWMs)i(are)e(deri)n(v)o (ed)f(from)g(an)i(alignment)e(of)i(all)1974 1029 y(these)f (identi\002ed)g(motif)f(sequences.)1926 1316 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 720 @rwi @setspecial %%BeginDocument: figure/factor_bcd.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 8 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.016560065029337 (G) numchar 0.0298081170528065 (A) numchar 0.0596162341056131 (T) numchar 0.0629282471114805 (C) numchar endstack (2) startstack 0.0160062448744909 (G) numchar 0.0480187346234726 (C) numchar 0.176068693619399 (A) numchar 0.576224815481671 (T) numchar endstack (3) startstack 0.0690711956332941 (G) numchar 1.6922442930157 (A) numchar endstack (4) startstack 2 (A) numchar endstack (5) startstack 0.36056805531517 (G) numchar 0.72113611063034 (T) numchar endstack (6) startstack 0.027469949007584 (A) numchar 0.13734974503792 (T) numchar 1.23614770534128 (C) numchar endstack (7) startstack 0.0111654664291333 (A) numchar 0.0446618657165333 (G) numchar 0.2344747950118 (T) numchar 0.279136660728333 (C) numchar endstack (8) startstack 0.0156313024016629 (A) numchar 0.0390782560041573 (T) numchar 0.0625252096066517 (C) numchar 0.0820643376087304 (G) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 700 w @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 720 @rwi @setspecial %%BeginDocument: figure/factor_cad.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 10 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.0183455572482361 (C) numchar 0.0366911144964723 (T) numchar 0.0372470404736915 (G) numchar 0.0744940809473831 (A) numchar endstack (2) startstack 0.00916621168189109 (C) numchar 0.018802485501315 (T) numchar 0.0190375165700815 (A) numchar 0.0235031068766438 (G) numchar endstack (3) startstack 0.00818833862956073 (C) numchar 0.00832257368906173 (G) numchar 0.00953068922457069 (A) numchar 0.0142289163071055 (T) numchar endstack (4) startstack 0.0321509672165251 (G) numchar 0.0401887090206563 (A) numchar 0.0544780277835563 (T) numchar 0.141107022783638 (C) numchar endstack (5) startstack 0.016600582423535 (T) numchar 0.0191063307138799 (C) numchar 0.019419549250173 (G) numchar 0.0388390985003459 (A) numchar endstack (6) startstack 0.0779491408105151 (G) numchar 0.17610731812746 (C) numchar 0.612045105623304 (T) numchar endstack (7) startstack 2 (A) numchar endstack (8) startstack 2 (A) numchar endstack (9) startstack 2 (A) numchar endstack (10) startstack 0.0225623547280353 (C) numchar 0.0459924923302257 (T) numchar 0.0616125840650194 (G) numchar 0.13016743112328 (A) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 2233 1339 a FG(bcd)569 b(cad)1926 1534 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 720 @rwi @setspecial %%BeginDocument: figure/factor_hb.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 11 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.0510955618516396 (G) numchar 0.0613146742219675 (C) numchar 0.0613146742219675 (A) numchar 0.301463814924674 (T) numchar endstack (2) startstack 2 (T) numchar endstack (3) startstack 0.0162466180450149 (A) numchar 0.0324932360900297 (G) numchar 0.0649864721800594 (C) numchar 1.39720915187128 (T) numchar endstack (4) startstack 2 (T) numchar endstack (5) startstack 2 (T) numchar endstack (6) startstack 0.0205834120157473 (C) numchar 1.89367390544875 (T) numchar endstack (7) startstack 0.0335578518483125 (T) numchar 0.0335578518483125 (C) numchar 0.0969449053395694 (G) numchar 0.182703860063035 (A) numchar endstack (8) startstack 0.0290214265792125 (G) numchar 0.0411136876538844 (C) numchar 0.0411136876538844 (A) numchar 0.113667254101916 (T) numchar endstack (9) startstack 0.0084764036872154 (A) numchar 0.0762876331849386 (C) numchar 0.118669651621016 (T) numchar 0.190719082962346 (G) numchar endstack (10) startstack 0.00366095793745781 (T) numchar 0.00516841120582279 (G) numchar 0.00538376167273208 (C) numchar 0.00581446260655064 (A) numchar endstack (11) startstack 0.0108341768339966 (A) numchar 0.0312987330759902 (C) numchar 0.0337063279279895 (G) numchar 0.0361139227799887 (T) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 700 w @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 720 @rwi @setspecial %%BeginDocument: figure/factor_kni.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 10 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 2 (A) numchar endstack (2) startstack 2 (A) numchar endstack (3) startstack 0.125809881109066 (G) numchar 0.125809881109066 (A) numchar 0.377429643327199 (C) numchar endstack (4) startstack 0.411619762218133 (G) numchar 0.617429643327199 (T) numchar endstack (5) startstack 0.255614381022528 (C) numchar 1.02245752409011 (A) numchar endstack (6) startstack 2 (G) numchar endstack (7) startstack 0.125809881109066 (G) numchar 0.125809881109066 (C) numchar 0.377429643327199 (A) numchar endstack (8) startstack 0.0956143810225276 (C) numchar 0.191228762045055 (T) numchar 0.191228762045055 (G) numchar endstack (9) startstack 2 (C) numchar endstack (10) startstack 2 (A) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 700 w @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 720 @rwi @setspecial %%BeginDocument: figure/factor_kr.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 10 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.0256124508815782 (T) numchar 0.0512249017631564 (C) numchar 0.0896435780855237 (G) numchar 0.204899607052626 (A) numchar endstack (2) startstack 0.0541028700353318 (G) numchar 0.0541028700353318 (C) numchar 1.46077749095396 (A) numchar endstack (3) startstack 0.0451484463588965 (T) numchar 0.13544533907669 (C) numchar 1.12871115897241 (A) numchar endstack (4) startstack 0.0289950607562243 (G) numchar 0.0386600810082991 (T) numchar 0.0676551417645234 (C) numchar 0.144975303781122 (A) numchar endstack (5) startstack 0.0615035540534047 (T) numchar 1.72209951349533 (G) numchar endstack (6) startstack 0.157258756177642 (A) numchar 1.36290922020623 (G) numchar endstack (7) startstack 0.0685747615356903 (C) numchar 0.171436903839226 (A) numchar 0.754322376892593 (G) numchar endstack (8) startstack 0.0615035540534047 (G) numchar 1.72209951349533 (T) numchar endstack (9) startstack 0.0262926332007347 (A) numchar 0.078877899602204 (C) numchar 0.105170532802939 (G) numchar 0.552145297215428 (T) numchar endstack (10) startstack 0.0294123920994624 (C) numchar 0.0882371762983872 (T) numchar 0.0882371762983872 (G) numchar 0.647072626188173 (A) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 2246 1558 a(hb)585 b(kni)628 b(kr)2073 1677 y Fw(Figure)22 b(5.)g FH(Berman)c(et)f(al.)f([2]')l(s)h(Drosophila)h (motif)f(patterns)h(deri)n(v)o(ed)2073 1752 y(from)f(multi-alignments)k (of)c(biologically)k(identi\002ed)e(motif)f(instances.)2024 2152 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 1008 @rwi @setspecial %%BeginDocument: figure/theta_motifdataII_m2_theta3_sepall.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 15 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.00865708208196707 (C) numchar 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numchar 0.0335812105838088 (G) numchar 0.045013112059148 (C) numchar 0.106459582489096 (T) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 939 w @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 1008 @rwi @setspecial %%BeginDocument: figure/theta_motifdataI_m3_theta4_sepall.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 18 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.0207660735176299 (C) numchar 0.0276880980235065 (A) numchar 0.0281495663238983 (G) numchar 0.0618367522524979 (T) numchar endstack (2) startstack 0.0134915268210166 (A) numchar 0.313677998588636 (G) numchar 0.684694986166592 (T) numchar endstack (3) startstack 0.00525943408790358 (A) numchar 0.120966984021782 (G) numchar 1.45160380826139 (C) numchar endstack (4) startstack 0.00352730386112768 (A) numchar 0.345675778390512 (G) numchar 0.708988076086663 (C) numchar endstack (5) startstack 0.0417531824370347 (G) numchar 0.0588340297976398 (C) numchar 0.0910978525898939 (T) numchar 0.377676513862268 (A) numchar endstack (6) startstack 0.0268141117196469 (T) numchar 0.0319215615710082 (C) numchar 0.158330945392201 (A) numchar 0.165992120169243 (G) numchar endstack (7) startstack 0.0233910230767246 (A) numchar 0.342093712497097 (C) numchar 0.51167862980335 (G) numchar endstack (8) startstack 0.0152783412606763 (G) numchar 0.0254639021011272 (C) numchar 0.0352250645732259 (A) numchar 0.0513522025706065 (T) numchar endstack (9) startstack 0.00571922728814999 (A) numchar 0.00898735716709284 (G) numchar 0.00957095178833264 (C) numchar 0.0107381410308122 (T) numchar endstack (10) startstack 0.0236348124385361 (C) numchar 0.0302000381159072 (G) numchar 0.051865282851232 (T) numchar 0.0912566369154588 (A) numchar endstack (11) startstack 0.00976232853474198 (G) numchar 0.0121052873830801 (A) numchar 0.015814972226282 (C) numchar 0.0208913830643478 (T) numchar endstack (12) startstack 0.00785636438175591 (A) numchar 0.263188206788823 (G) numchar 0.907410086092807 (C) numchar endstack (13) startstack 0.00495105198349608 (A) numchar 0.11387419562041 (G) numchar 0.116349721612158 (T) numchar 0.507482828308348 (C) numchar endstack (14) startstack 0.101365814513827 (G) numchar 0.15594740694435 (A) numchar 0.327489554583134 (C) numchar endstack (15) startstack 0.0109103429143417 (C) numchar 0.0323548100218408 (T) numchar 0.0323548100218408 (G) numchar 0.0372456533972353 (A) numchar endstack (16) startstack 0.176476696165516 (A) numchar 1.29416243854712 (T) numchar endstack (17) startstack 0.0442377834127337 (G) numchar 0.0565260565829375 (A) numchar 0.103221494629712 (C) numchar 0.533311055586845 (T) numchar endstack (18) startstack 0.0178196957054652 (T) numchar 0.0201732404212813 (G) numchar 0.0205094610949693 (A) numchar 0.0423638048846908 (C) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 2429 2187 a FG(1)911 b(2)2024 2448 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 1008 @rwi @setspecial %%BeginDocument: figure/theta_motifdataI_m2_theta1_sepall.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 10 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.00295814437372306 (G) numchar 0.0118325774948923 (A) numchar 0.399349490452614 (C) numchar 0.47330309979569 (T) numchar endstack (2) startstack 0.0177942262869832 (A) numchar 0.0444855657174579 (G) numchar 0.18461509772745 (T) numchar 0.420388596029977 (C) numchar endstack (3) startstack 0.0191920686410409 (A) numchar 1.90001479546305 (T) numchar endstack (4) startstack 0.00470334123082513 (A) numchar 0.18343030800218 (T) numchar 1.22286872001453 (C) numchar endstack (5) startstack 0.04293874943955 (A) numchar 1.79729336939831 (G) numchar endstack (6) startstack 0.106049379088351 (A) numchar 0.150100659632743 (T) numchar 0.233308633994373 (C) numchar endstack (7) startstack 0.0573090787890128 (G) numchar 0.0590999875011694 (A) numchar 0.066263622349796 (C) numchar 0.354599925007017 (T) numchar endstack (8) startstack 0.0175031013241342 (A) numchar 0.0525093039724026 (C) numchar 0.154027291652381 (G) numchar 0.301053342775108 (T) numchar endstack (9) startstack 0.0211294740166442 (G) numchar 0.0456396638759514 (A) numchar 0.0625432430892668 (C) numchar 0.124241307217868 (T) numchar endstack (10) startstack 0.00547000114197467 (G) numchar 0.00772235455337601 (C) numchar 0.00943843334301512 (T) numchar 0.00954568826736757 (A) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 939 w @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 1008 @rwi @setspecial %%BeginDocument: figure/thetaI1.fake.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 15 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.0253045595145513 (A) numchar 1.8725374040768 (T) numchar endstack (2) startstack 0.0245913634857315 (T) numchar 0.0302662935209003 (A) numchar 0.206189124611133 (G) numchar 0.306446221899115 (C) numchar endstack (3) startstack 0.00873899111550603 (A) numchar 0.0129264243583527 (G) numchar 0.0136546736179782 (T) numchar 0.0192986053800758 (C) numchar endstack (4) startstack 0.0441773358950848 (A) numchar 0.132532007685254 (G) numchar 1.1486107332722 (C) numchar endstack (5) startstack 0.00514320583326693 (A) numchar 0.13372335166494 (C) numchar 1.40409519248187 (G) numchar endstack (6) startstack 0.0065592321492941 (A) numchar 1.96121041263894 (G) numchar endstack (7) startstack 0.00452904102918001 (T) numchar 0.203806846313101 (A) numchar 1.15037642141172 (C) numchar endstack (8) startstack 0.00791414026498682 (C) numchar 0.00832349234765856 (T) numchar 0.0105067034552411 (A) numchar 0.0141908721992867 (G) numchar endstack (9) startstack 0.00945376796134786 (G) numchar 0.0740545156972249 (C) numchar 0.0756301436907829 (T) numchar 0.0772057716843409 (A) numchar endstack (10) startstack 0.0333267307964339 (A) numchar 0.0343366317296592 (C) numchar 0.0767524709251205 (G) numchar 0.158554446516367 (T) numchar endstack (11) startstack 0.0157293442783987 (A) numchar 0.059968125061395 (T) numchar 0.0766805533571936 (C) numchar 0.142547182522988 (G) numchar endstack (12) startstack 0.0149211936854775 (T) numchar 0.0516502858343451 (A) numchar 0.122812901872776 (G) numchar 0.154950857503035 (C) numchar endstack (13) startstack 0.0224244316868369 (G) numchar 0.0229459300981586 (C) numchar 0.0432843681397083 (T) numchar 0.0677947934718323 (A) numchar endstack (14) startstack 0.0471935950578739 (T) numchar 0.0510201027652691 (C) numchar 0.0573976156109278 (G) numchar 0.227039457305448 (A) numchar endstack (15) startstack 0.00366049437823247 (C) numchar 0.0512469212952545 (G) numchar 0.164722247020461 (A) numchar 0.878518650775792 (T) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 2429 2484 a(3)921 b(4)2024 2744 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 1008 @rwi @setspecial %%BeginDocument: figure/thetaII1.fake.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 20 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.00808263552463 (C) numchar 0.100224680505412 (T) numchar 0.10507426182019 (G) numchar 0.271576553627568 (A) numchar endstack (2) startstack 0.00131202363189303 (G) numchar 0.120706174134159 (A) numchar 0.124642245029838 (C) numchar 0.146946646772019 (T) numchar endstack (3) startstack 0.00535190785532696 (A) numchar 0.00678545460228953 (G) numchar 0.00716773373481289 (T) numchar 0.00936583874682217 (C) numchar endstack (4) startstack 0.0326273840483641 (G) numchar 0.0355935098709427 (T) numchar 0.154238542774085 (A) numchar 0.667378310080175 (C) numchar endstack (5) startstack 0.0461451988205085 (C) numchar 0.0678605865007478 (T) numchar 0.0868615507209572 (G) numchar 0.61345970196676 (A) numchar endstack (6) startstack 0.0264177031535996 (G) numchar 0.0458833791615152 (T) numchar 0.112622839760083 (C) numchar 0.232197706665849 (A) numchar endstack (7) startstack 0.0513639612035345 (G) numchar 0.0629622750236875 (C) numchar 0.0629622750236875 (A) numchar 0.31978208104136 (T) numchar endstack (8) startstack 0.0118395288048595 (G) numchar 0.0246938743644212 (A) numchar 0.0274000523769605 (C) numchar 0.0375482199239828 (T) numchar endstack (9) startstack 0.0192696896641949 (C) numchar 0.0545974540485523 (G) numchar 0.0835019885448448 (T) numchar 0.163792362145657 (A) numchar endstack (10) startstack 0.0214317733083169 (C) numchar 0.0385771919549705 (G) numchar 0.118946341861159 (A) numchar 0.142521292500308 (T) numchar endstack (11) startstack 0.0255350404819369 (A) numchar 0.0276629605220983 (C) numchar 0.0631282945247884 (G) numchar 0.0964657084873171 (T) numchar endstack (12) startstack 0.0189726309726411 (G) numchar 0.0591499671499988 (T) numchar 0.0825867465867908 (A) numchar 0.174101790101883 (C) numchar endstack (13) startstack 0.017165040814105 (C) numchar 0.0444271644600365 (T) numchar 0.114097035999639 (A) numchar 0.127223243681014 (G) numchar endstack (14) startstack 0.00681900182432641 (C) numchar 0.00960226787507188 (T) numchar 0.0122463706232801 (A) numchar 0.0130813504385037 (G) numchar endstack (15) startstack 0.0109953961840642 (G) numchar 0.0598638236687941 (T) numchar 0.13927501833148 (A) numchar 0.156378967951136 (C) numchar endstack (16) startstack 0.00395233287310926 (C) numchar 0.090903656081513 (T) numchar 0.0948559889546223 (G) numchar 0.995987884023534 (A) numchar endstack (17) startstack 0.299815259638364 (A) numchar 0.883666028407808 (T) numchar endstack (18) startstack 0.0321088676758175 (T) numchar 0.0682313438111122 (G) numchar 0.0682313438111122 (C) numchar 1.03551098254511 (A) numchar endstack (19) startstack 0.0113842842948138 (G) numchar 0.0113842842948138 (C) numchar 0.0455371371792553 (T) numchar 1.63933693845319 (A) numchar endstack (20) startstack 0.00725769822371516 (G) numchar 0.0580615857897213 (C) numchar 0.145153964474303 (T) numchar 0.878181485069534 (A) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 939 w @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 1008 @rwi @setspecial %%BeginDocument: figure/thetaIII2.fake.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 10 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.353089839822243 (A) numchar 0.738940592617684 (T) numchar endstack (2) startstack 0.00751388344483204 (G) numchar 0.0676249510034883 (C) numchar 0.123979076839729 (T) numchar 0.927964605436757 (A) numchar endstack (3) startstack 0.00602439730206541 (C) numchar 0.051207377067556 (G) numchar 0.192780713666093 (T) numchar 0.653647107274097 (A) numchar endstack (4) startstack 0.0148536968481936 (G) numchar 0.0445610905445809 (T) numchar 0.0594147873927745 (C) numchar 1.36654011003381 (A) numchar endstack (5) startstack 0.0113842842948138 (G) numchar 0.0113842842948138 (C) numchar 0.0455371371792553 (T) numchar 1.63933693845319 (A) numchar endstack (6) startstack 0.010801491401855 (C) numchar 0.0162022371027825 (G) numchar 0.0648089484111301 (T) numchar 1.52841103336248 (A) numchar endstack (7) startstack 0.264288624614433 (A) numchar 0.994228635454294 (T) numchar endstack (8) startstack 0.0108761280235264 (A) numchar 0.0569397290643443 (C) numchar 0.0614181347210904 (G) numchar 0.0626976791944465 (T) numchar endstack (9) startstack 0.0187689034682062 (C) numchar 0.0693005666518384 (G) numchar 0.0981758027567711 (A) numchar 0.246883268697174 (T) numchar endstack (10) startstack 0.0118248719346669 (C) numchar 0.0325183978203339 (T) numchar 0.218760130791337 (G) numchar 0.623761994553677 (A) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 2429 2780 a(5)911 b(6)2024 3040 y @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 1008 @rwi @setspecial %%BeginDocument: figure/thetaI3.fake.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 15 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.378108953766801 (A) numchar 0.682009608196192 (T) numchar endstack (2) startstack 0.013254780108625 (G) numchar 0.0747087606122502 (C) numchar 0.0891685207307502 (T) numchar 0.184361941510875 (A) numchar endstack (3) startstack 0.0137461194554066 (G) numchar 0.0528696902131021 (A) numchar 0.116313318468825 (T) numchar 0.134289013141279 (C) numchar endstack (4) startstack 0.0311340852095677 (A) numchar 0.075377258928427 (T) numchar 0.0770158949920885 (G) numchar 0.308063579968354 (C) numchar endstack (5) startstack 0.0262812694510521 (T) numchar 0.0431763712410142 (G) numchar 0.0666417903937393 (A) numchar 0.145485598746896 (C) numchar endstack (6) startstack 0.0452936070165252 (T) numchar 0.0452936070165252 (G) numchar 0.11117521722238 (C) numchar 0.415877664424458 (A) numchar endstack (7) startstack 0.0127608096959839 (C) numchar 0.0552968420159302 (G) numchar 0.154547584095805 (T) numchar 0.202755087391744 (A) numchar endstack (8) startstack 0.00570203679450766 (A) numchar 0.0741264783285996 (G) numchar 1.63078252322919 (C) numchar endstack (9) startstack 0.0065592321492941 (A) numchar 1.96121041263894 (C) numchar endstack (10) startstack 0.0065592321492941 (A) numchar 1.96121041263894 (C) numchar endstack (11) startstack 0.0728998888575946 (T) numchar 0.214411437816455 (G) numchar 0.355922986775315 (A) numchar endstack (12) startstack 0.00420734490072347 (G) numchar 0.0778358806633841 (C) numchar 0.168293796028939 (T) numchar 0.380764713515474 (A) numchar endstack (13) startstack 0.08999031472004 (C) numchar 0.139984934008951 (A) numchar 0.769917137049231 (T) numchar endstack (14) startstack 0.0065592321492941 (A) numchar 1.96121041263894 (C) numchar endstack (15) startstack 0.00575224700906458 (A) numchar 0.0690269641087749 (G) numchar 1.65089489160153 (C) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 939 w @beginspecial 0 @llx 0 @lly 510 @urx 141 @ury 1008 @rwi @setspecial %%BeginDocument: figure/thetaIII3.fake.fasta.eps %!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: %%Creator: seqlogo (1.0) %%CreationDate: %%BoundingBox: 0 0 510 141 %%Pages: 0 %%DocumentFonts: %%EndComments % * seq_1 % * seq_2 % * seq_3 % * seq_4 % * seq_5 % * seq_6 % * seq_7 % * seq_8 % * seq_9 % * seq_10 % * seq_11 % * seq_12 % * seq_13 % * seq_14 % * seq_15 % * seq_16 % * seq_17 % * seq_18 % * seq_19 % * seq_20 % * seq_21 % * seq_22 % * seq_23 % * seq_24 % * seq_25 % * seq_26 % * seq_27 % * seq_28 % * seq_29 % * seq_30 % * seq_31 % * seq_32 % * seq_33 % * seq_34 % * seq_35 % * seq_36 % * seq_37 % * seq_38 % * seq_39 % * seq_40 % * seq_41 % * seq_42 % * seq_43 % * seq_44 % * seq_45 % * seq_46 % * seq_47 % * seq_48 % * seq_49 % * seq_50 % * seq_51 % * seq_52 % * seq_53 % * seq_54 % * seq_55 % * seq_56 % * seq_57 % * seq_58 % * seq_59 % * seq_60 % * seq_61 % * seq_62 % * seq_63 % * seq_64 % * seq_65 % * seq_66 % * seq_67 % * seq_68 % * seq_69 % * seq_70 % * seq_71 % * seq_72 % * seq_73 % * seq_74 % * seq_75 % * seq_76 % * seq_77 % * seq_78 % * seq_79 % * seq_80 % * seq_81 % * seq_82 % * seq_83 % * seq_84 % * seq_85 % * seq_86 % * seq_87 % * seq_88 % * seq_89 % * seq_90 % * seq_91 % * seq_92 % * seq_93 % * seq_94 % * seq_95 % * seq_96 % * seq_97 % * seq_98 % * seq_99 % * seq_100 % * seq_101 % * seq_102 % * seq_103 % * seq_104 % * seq_105 % * seq_106 % * seq_107 % * seq_108 % * seq_109 % * seq_110 % * seq_111 % * seq_112 % * seq_113 % * seq_114 % * seq_115 % * seq_116 % * seq_117 % * seq_118 % * seq_119 % * seq_120 % * seq_121 % * seq_122 % * seq_123 % * seq_124 % * seq_125 % * seq_126 % * seq_127 % * seq_128 % * seq_129 % * seq_130 % * seq_131 % * seq_132 % * seq_133 % * seq_134 % * seq_135 % * seq_136 % * seq_137 % * seq_138 % * seq_139 % * seq_140 % * seq_141 % * seq_142 % * seq_143 % * seq_144 % * seq_145 % * seq_146 % * seq_147 % * seq_148 % * seq_149 % * seq_150 % * seq_151 % * seq_152 % * seq_153 % * seq_154 % * seq_155 % * seq_156 % * seq_157 % * seq_158 % * seq_159 % * seq_160 % * seq_161 % * seq_162 % * seq_163 % * seq_164 % * seq_165 % * seq_166 % * seq_167 % * seq_168 % * seq_169 % * seq_170 % * seq_171 % * seq_172 % * seq_173 % * seq_174 % * seq_175 % * seq_176 % * seq_177 % * seq_178 % * seq_179 % * seq_180 % * seq_181 % * seq_182 % * seq_183 % * seq_184 % * seq_185 % * seq_186 % * seq_187 % * seq_188 % * seq_189 % * seq_190 % * seq_191 % * seq_192 % * seq_193 % * seq_194 % * seq_195 % * seq_196 % * seq_197 % * seq_198 % * seq_199 % * seq_200 % * seq_201 % * seq_202 % * seq_203 % * seq_204 % * seq_205 % * seq_206 % * seq_207 % * seq_208 % * seq_209 % * seq_210 % * seq_211 % * seq_212 % * seq_213 % * seq_214 % * seq_215 % * seq_216 % * seq_217 % * seq_218 % * seq_219 % * seq_220 % * seq_221 % * seq_222 % * seq_223 % * seq_224 % * seq_225 % * seq_226 % * seq_227 % * seq_228 % * seq_229 % * seq_230 % * seq_231 % * seq_232 % * seq_233 % * seq_234 % * seq_235 % * seq_236 % * seq_237 % * seq_238 % * seq_239 % * seq_240 % * seq_241 % * seq_242 % * seq_243 % * seq_244 % * seq_245 % * seq_246 % * seq_247 % * seq_248 % * seq_249 % * seq_250 % * seq_251 % * seq_252 % * seq_253 % * seq_254 % * seq_255 % * seq_256 % * seq_257 % * seq_258 % * seq_259 % * seq_260 % * seq_261 % * seq_262 % * seq_263 % * seq_264 % * seq_265 % * seq_266 % * seq_267 % * seq_268 % * seq_269 % * seq_270 % * seq_271 % * seq_272 % * seq_273 % * seq_274 % * seq_275 % * seq_276 % * seq_277 % * seq_278 % * seq_279 % * seq_280 % * seq_281 % * seq_282 % * seq_283 % * seq_284 % * seq_285 % * seq_286 % * seq_287 % * seq_288 % * seq_289 % * seq_290 % * seq_291 % * seq_292 % * seq_293 % * seq_294 % * seq_295 % * seq_296 % * seq_297 % * seq_298 % * seq_299 % * seq_300 % * NUCLEOTIDE ALIGNMENT % ---- CONSTANTS ---- /cmfactor 72 2.54 div def % defines points -> cm conversion /cm {cmfactor mul} bind def % defines centimeters % ---- VARIABLES ---- /black [0 0 0] def /red [0.8 0 0] def /green [0 0.8 0] def /blue [0 0 0.8] def /yellow [1 0.71 .0] def /purple [0.8 0 0.8] def /orange [1 0.7 0] def /logoWidth 18 cm def /logoHeight 5 cm def /logoTitle () def /yaxis true def /yaxisLabel (bits) def /yaxisBits 2 def % bits /xaxis true def /xaxisLabel ( ) def /showEnds (d) def % d: DNA, p: PROTEIN, -: none /showFineprint true def /fineprint () def /charsPerLine 10 def /logoLines 1 def /showingBox (n) def %n s f /shrinking false def /shrink 1 def /outline false def /IbeamFraction 1 def /IbeamGray 0.75 def /IbeamLineWidth 0.5 def /fontsize 12 def /titleFontsize 14 def /smallFontsize 6 def /defaultColor black def % Standard DNA/RNA color scheme /colorDict << (G) orange (T) red (C) blue (A) green (U) red >> def % Standard DNA/RNA color scheme % /colorDict << % (G) orange % (T) red % (C) blue % (A) green % (U) red % >> def % Standard Amino Acid colors %/colorDict << % (G) green % (S) green % (T) green % (Y) green % (C) green % (N) purple % (Q) purple % (K) blue % (R) blue % (H) blue % (D) red % (E) red % (P) black % (A) black % (W) black % (F) black % (L) black % (I) black % (M) black % (V) black %>> def % ---- DERIVED PARAMETERS ---- /leftMargin fontsize 2.5 mul def /bottomMargin fontsize 0.75 mul % Add extra room for axis xaxis {fontsize 1.75 mul add } if xaxisLabel () eq {} {fontsize 0.75 mul add} ifelse def /topMargin logoTitle () eq { 10 }{titleFontsize 4 add} ifelse def /rightMargin %Add extra room if showing ends showEnds (-) eq { fontsize}{fontsize 1.5 mul} ifelse def /yaxisHeight logoHeight bottomMargin sub topMargin sub def /ticWidth fontsize 2 div def /pointsPerBit yaxisHeight yaxisBits div def /isBoxed showingBox (s) eq showingBox (f) eq or { true } { false } ifelse def /stackMargin 1 def % Do not add space aroung characters if characters are boxed /charRightMargin isBoxed { 0.0 } {stackMargin} ifelse def /charTopMargin isBoxed { 0.0 } {stackMargin} ifelse def /charWidth logoWidth leftMargin sub rightMargin sub charsPerLine div charRightMargin sub def /charWidth4 charWidth 4 div def /charWidth2 charWidth 2 div def /stackWidth charWidth charRightMargin add def /numberFontsize fontsize charWidth lt {fontsize}{charWidth} ifelse def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.5 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % Outline width is proporional to charWidth, % but no less that 1 point /outlinewidth charWidth 32 div dup 1 gt {}{pop 1} ifelse def % ---- PROCEDURES ---- /StartLogo { % Save state save gsave % Print Logo Title, top center gsave SetTitleFont logoWidth 2 div logoTitle stringwidth pop 2 div sub logoHeight logoLines mul titleFontsize sub moveto logoTitle show grestore % Print X-axis label, bottom center gsave SetStringFont logoWidth 2 div xaxisLabel stringwidth pop 2 div sub fontsize 3 div moveto xaxisLabel show grestore % Show Fine Print showFineprint { gsave SetSmallFont logoWidth fineprint stringwidth pop sub smallFontsize sub smallFontsize 3 div moveto fineprint show grestore } if % Move to lower left corner of last line, first stack leftMargin bottomMargin translate % Move above first line ready for StartLine 0 logoLines logoHeight mul translate SetLogoFont } bind def /EndLogo { grestore showpage restore } bind def /StartLine{ % move down to the bottom of the line: 0 logoHeight neg translate gsave yaxis { MakeYaxis } if xaxis { ShowLeftEnd } if } bind def /EndLine{ xaxis { ShowRightEnd } if grestore } bind def /MakeYaxis { gsave stackMargin neg 0 translate ShowYaxisBar ShowYaxisLabel grestore } bind def /ShowYaxisBar { gsave SetStringFont /str 10 string def % string to hold number /smallgap stackMargin 2 div def % Draw first tic and bar gsave ticWidth neg 0 moveto ticWidth 0 rlineto 0 yaxisHeight rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 1 yaxisBits abs cvi {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def numberwidth % move back width of number neg loopnumber pointsPerBit mul % shift on y axis halfnumberheight sub % down half the digit moveto % move back the width of the string ticWidth neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again ticWidth 0 rlineto stroke } for grestore } bind def /ShowYaxisLabel { gsave SetStringFont ticWidth neg 2.75 mul yaxisHeight yaxisLabel stringwidth pop sub 2 div translate 90 rotate 0 0 moveto yaxisLabel show grestore } bind def /StartStack { % startstack xaxis {MakeNumber}{pop} ifelse gsave } bind def /EndStack { grestore stackWidth 0 translate } bind def % Draw a character whose height is proportional to symbol bits /MakeSymbol{ % charbits character MakeSymbol gsave /char exch def /bits exch def /bitsHeight bits pointsPerBit mul def /charHeight bitsHeight charTopMargin sub dup 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero def charHeight 0.0 gt { char SetColor charWidth charHeight char ShowChar showingBox (s) eq { % Unfilled box 0 0 charWidth charHeight false ShowBox } if showingBox (f) eq { % Filled box 0 0 charWidth charHeight true ShowBox } if } if grestore 0 bitsHeight translate } bind def /ShowChar { % ShowChar gsave /tc exch def % The character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def % if ysize is negative, make everything upside down! ysize 0 lt { % put ysize normal in this orientation /ysize ysize abs def xsize ysize translate 180 rotate } if shrinking { xsize 1 shrink sub 2 div mul ysize 1 shrink sub 2 div mul translate shrink shrink scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } % end if {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } % end if {pop pop} ifelse grestore } repeat % Adjust horizontal position if the symbol is an I tc (I) eq { charWidth 2 div % half of requested character width tc CharBoxWidth 2 div % half of the actual character sub 0 translate % Avoid x scaling for I /xmulfactor 1 def } if % ---- Finally, draw the character newpath xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg moveto outline { % outline characters: outlinewidth setlinewidth tc true charpath gsave 1 setgray fill grestore clip stroke } { % regular characters tc show } ifelse grestore } bind def /ShowBox { % x1 y1 x2 y2 filled ShowBox gsave /filled exch def /y2 exch def /x2 exch def /y1 exch def /x1 exch def newpath x1 y1 moveto x2 y1 lineto x2 y2 lineto x1 y2 lineto closepath clip filled { fill }{ 0 setgray stroke } ifelse grestore } bind def /MakeNumber { % number MakeNumber gsave SetNumberFont stackWidth 0 translate 90 rotate % rotate so the number fits dup stringwidth pop % find the length of the number neg % prepare for move stackMargin sub % Move back a bit charWidth (0) CharBoxHeight % height of numbers sub 2 div % moveto % move back to provide space show grestore } bind def /Ibeam{ % heightInBits Ibeam gsave % Make an Ibeam of twice the given height in bits /height exch pointsPerBit mul def /heightDRAW height IbeamFraction mul def IbeamLineWidth setlinewidth IbeamGray setgray charWidth2 height neg translate ShowIbar newpath 0 0 moveto 0 heightDRAW rlineto stroke newpath 0 height moveto 0 height rmoveto currentpoint translate ShowIbar newpath 0 0 moveto 0 heightDRAW neg rlineto currentpoint translate stroke grestore } bind def /ShowIbar { % make a horizontal bar gsave newpath charWidth4 neg 0 moveto charWidth4 0 lineto stroke grestore } bind def /ShowLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY moveto showEnds (d) eq {(5) show ShowPrime} if showEnds (p) eq {(N) show} if grestore } bind def /ShowRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY moveto showEnds (d) eq {(3) show ShowPrime} if showEnds (p) eq {(C) show} if grestore } bind def /ShowPrime { gsave SetPrimeFont (\242) show grestore } bind def /SetColor{ % SetColor dup colorDict exch known { colorDict exch get aload pop setrgbcolor } { pop defaultColor aload pop setrgbcolor } ifelse } bind def % define fonts /SetTitleFont {/Times-Bold findfont titleFontsize scalefont setfont} bind def /SetLogoFont {/Helvetica-Narrow-Bold findfont charWidth scalefont setfont} bind def /SetStringFont{/Helvetica-Bold findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/Helvetica findfont smallFontsize scalefont setfont} bind def /SetNumberFont { /Helvetica-Bold findfont numberFontsize scalefont setfont } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def % Deprecated names /startstack {StartStack} bind def /endstack {EndStack} bind def /makenumber {MakeNumber} bind def /numchar { MakeSymbol } bind def %%EndProlog %%Page: 1 1 StartLogo StartLine % line number 1 (1) startstack 0.0127376219039173 (A) numchar 0.0409819139517338 (C) numchar 0.0498428683196763 (T) numchar 0.0625804902235935 (G) numchar endstack (2) startstack 0.0065592321492941 (A) numchar 1.96121041263894 (C) numchar endstack (3) startstack 0.0065592321492941 (A) numchar 1.96121041263894 (C) numchar endstack (4) startstack 0.0756273745914915 (T) numchar 0.190372356730306 (A) numchar 0.516352419624666 (G) numchar endstack (5) startstack 0.0124929658270198 (A) numchar 0.220709062944016 (C) numchar 1.01609455393094 (G) numchar endstack (6) startstack 0.0338313849395402 (T) numchar 0.0338313849395402 (A) numchar 0.0968277568959255 (G) numchar 0.185489317427134 (C) numchar endstack (7) startstack 0.0352585444881256 (A) numchar 0.043093776596598 (T) numchar 0.131240137816912 (C) numchar 0.378049949233791 (G) numchar endstack (8) startstack 0.0194654954185813 (T) numchar 0.0629766028248219 (G) numchar 0.0790070108165947 (C) numchar 0.182059633620849 (A) numchar endstack (9) startstack 0.0163902989525562 (C) numchar 0.0389976078526338 (A) numchar 0.0406931560201396 (G) numchar 0.073473753925252 (T) numchar endstack (10) startstack 0.0065592321492941 (A) numchar 1.96121041263894 (C) numchar endstack EndLine EndLogo %%EOF %%EndDocument @endspecial 2429 3076 a(7)g(8)2073 3231 y Fw(Figure)22 b(6.)g FH(Motif)c(patterns)g(detected)h(by)e Fv(LOGOS)e FH(in)i(the)g(re)o(gulatory)2073 3306 y(re)o(gions)i(of)e(9)f (Drosophila)j(genes.)2073 3527 y FJ(W)-7 b(e)28 b(apply)d FK(LOGOS)h FJ(\(which)f(is)i(set)g(to)f(identify)f(4)h(motifs)g(at)1974 3621 y(a)e(time\))g(to)h(the)f(Drosophila)f(dataset)h(and)g(Figure)f(6) h(gi)n(v)o(es)g(a)h(par)n(-)1974 3716 y(tial)30 b(list)h(of)e(the)h (top-scoring)e(\(data)h(lik)o(elihood)f(under)g(the)i FK(LO-)1974 3811 y(GOS)17 b FJ(model\))g(motif)g(patterns.)23 b(Note)18 b(that)g(the)g FL(lo)o(gos)f FJ(sho)n(wn)g(here)1974 3905 y(are)k(not)f(the)h(con)m(v)o(entional)d(sequence)i FL(lo)o(gos)h FJ(based)g(on)f(counts)g(of)1974 4000 y(aligned)27 b(nucleotides;)32 b(instead)c(we)h(use)g(the)f FL(lo)o(go)g FJ(visualization)1974 4095 y(softw)o(are)j(to)g(graphically)e(present)i (the)g FK(Bay)o(esian)h(estimate)e FJ(of)1974 4189 y(the)21 b(position-speci\002c)f(multinomial)f(parameters)h FC(\022)k FJ(of)d(each)g(mo-)1974 4284 y(tif,)e(so)h(the)o(y)e(are)h(not)f (necessarily)h(equal)f(to)h(the)g(usual)g(nt)g(frequen-)1974 4379 y(cies)f(of)g(aligned)f(sequences,)g(b)n(ut)h(represent)f(a)h (more)f(rob)n(ust)h(prob-)1974 4473 y(abilistic)23 b(model)e(of)h(the)g (motif)g(sequences.)30 b(A)22 b(visual)g(inspection)1974 4568 y(re)n(v)o(eals)j(that)h(patterns)f(1)h(and)f(5)h(correspond)d(to) j(the)f FL(hb)h FJ(and)f FL(cad)1974 4662 y FJ(binding)16 b(sites)k(\(as)f(con\002rmed)d(by)i(the)g(matching)f(of)h(the)h (locations)1974 4757 y(of)28 b(our)g(results)h(and)f(the)h(sequence)e (annotations\).)48 b(P)o(art)29 b(of)g(pat-)1974 4852 y(tern)d(2)h(agrees)f(with)g(the)h(re)n(v)o(erse)e(complement)g(of)h (the)g FL(kr)i FJ(motif)1974 4946 y(\(containing)22 b(-CCCxTT)-8 b(-\),)26 b(b)n(ut)f(this)h(motif)e(seem)h(to)g(be)g(actually)1974 5041 y(a)e(\223tw)o(o-block\224)e(motif)h(because)g(the)g(pattern)g(we) h(detected)f(under)1974 5136 y(a)27 b(longer)f(estimated)h(motif)f (length)h(contains)f(an)h(additional)f(co-)1974 5230 y(occurring)d(conserv)o(ed)f(pattern)i(a)i(fe)n(w)f(bases)g(upstream.) 38 b(P)o(art)25 b(of)1974 5325 y(pattern)k(7)g(is)i(close)f(to)f(the)h FL(bcd)f FJ(motif)g(\(containing)f(-AA)-9 b(TCC-\))p eop %%Page: 10 10 10 9 bop -182 83 a FJ(b)n(ut)21 b(also)h(contains)e(additional)g(sites) j(\(i.e.,)e(the)g(three)g(highly)f(con-)-182 178 y(serv)o(ed)27 b(C')-5 b(s)29 b(upstream\).)47 b(A)28 b(careful)f(e)o(xamination)f(of) i(pattern)f(6)-182 272 y(suggests)19 b(that)h(it)g(may)f(be)h(actually) f(deri)n(v)o(ed)f(from)g(putati)n(v)o(e)g(motif)-182 367 y(subsequences)23 b(that)i(correspond)d(to)k(the)e FL(kni)h FJ(binding)f(site.)40 b(This)-182 462 y(is)18 b(not)g(ob)o(vious)e(at)i(\002rst)g(because)f(it)i(appears)e(quite)g (dif)n(ferent)f(from)-182 556 y(the)g FL(kni)h(lo)o(go)g FJ(in)g(Figure)f(5.)24 b(But)17 b(after)f(seeing)h(an)g(e)o(xample)e FL(kni)i FJ(site)-182 651 y(in)k(stripe2/7:)26 b(5'agaaaactagatca3',)17 b(starting)j(at)i(position)e(35,)h(we)-182 746 y(realized)28 b(that)g(the)h(answer)f(might)g(be)h(plausible.)50 b(The)28 b(discrep-)-182 840 y(anc)o(y)22 b(is)j(lik)o(ely)e(due)h(to)f(the)h (artif)o(acts)g(in)g(the)f(original)g(generation)-182 935 y(of)i(the)h(alignment)f(data)h(supporting)e(the)i FL(kni)g(lo)o(go)p FJ(:)36 b(only)25 b(5)i(bio-)-182 1029 y(logically)e(identi\002ed)h(instances)h(were)f(used)h(and)f(the)o (y)g(are)g(quite)-182 1124 y(di)n(v)o(erse;)39 b(the)34 b(resulting)f(multiple)g(alignment)f(is)j(visually)e(sub-)-182 1219 y(optimal)18 b(in)i(that)g(homogeneous)c(sites)21 b(are)f(se)n(v)o(erely)e(interspersed)-182 1313 y(with)26 b(heterogeneous)c(sites.)43 b(P)o(atterns)26 b(3,)h(4,)g(and)e(8)h(are) f(putati)n(v)o(e)-182 1408 y(motifs)j(not)g(annotated)f(in)i(the)g (input)f(sequences.)49 b(W)-7 b(e)30 b(also)f(ran)-182 1503 y(the)19 b(same)g(dataset)g(through)e(MEME)i(and)f(the)h(output)f (\(not)h(sho)n(wn)-182 1597 y(here\))i(is)i(much)e(weak)o(er)g(and)g (harder)g(to)h(interpret.)29 b(Note)22 b(that)g(the)-182 1692 y(motif)i(logos)h(gi)n(v)o(en)f(in)h(Figure)f(5)h(are)g(based)g (on)g(the)g(nucleotide-)-182 1787 y(frequenc)o(y)20 b(pro\002les)j(of)g (biologically)f(identi\002ed)h(instances)g(from)-182 1881 y(man)o(y)29 b(sources.)56 b(Thus)31 b(it)g(is)h(not)e(surprising) g(that)h(some)f(of)h(the)-182 1976 y(patterns)20 b(we)i(found)e(are)h (similar)h(b)n(ut)f(do)g(not)g(match)g(the)h FL(lo)o(gos)f FJ(in)-182 2071 y(Figure)f(5)i(e)o(xactly)e(since)i(our)f(logos)g(are)g (deri)n(v)o(ed)f(from)g(Bayesian)-182 2165 y(estimates)j(of)g(the)g (motif)f(parameters)g(and)h(our)f(data)h(source)f(con-)-182 2260 y(sists)28 b(of)f(the)h(4)f(re)o(gulatory)e(re)o(gions)h(of)h(the) g FL(e)o(ven-skipped)e FJ(gene,)-182 2354 y(which)17 b(might)h(be)g(smaller)g(and)g(less)h(representati)n(v)o(e)e(compared)f (to)-182 2449 y(the)k(data)g(source)f(underlying)f(Figure)h(5)i(\(e)o (xcept)d(for)i FL(kni)p FJ(\).)-182 2665 y FM(5)99 b(Conclusions)-83 2864 y FJ(W)-7 b(e)27 b(ha)n(v)o(e)e(presented)g(a)h(principled)e (generati)n(v)o(e)f(probabilistic)-182 2959 y(frame)n(w)o(ork)k(for)i (modeling)e(motifs)j(in)f(biopolymer)e(sequences.)-182 3054 y(A)21 b(modular)f(architecture)f(is)j(proposed,)d(which)i (consists)h(of)f(a)g(lo-)-182 3148 y(cal)g(submodel)e(of)h(motif)g (alignment,)f(and)h(a)h(global)f(submodel)f(of)-182 3243 y(motif)g(distrib)n(ution.)-83 3337 y(W)-7 b(e)39 b(use)f(an)f(HMDM)h (model)f(for)g(local)g(motif)h(alignment,)-182 3432 y(which)27 b(captures)g(site)i(dependencies)d(inside)i(motifs)f(and)h(incor)n(-) -182 3527 y(porates)g(learnable)g(prior)g(kno)n(wledge)e(from)i(kno)n (wn)g(motifs)h(for)-182 3621 y(Bayesian)17 b(estimation)f(of)h(the)g (PWMs)h(of)f(no)o(v)o(el)f(motifs)h(in)g(unseen)-182 3716 y(sequences.)57 b(W)-7 b(e)32 b(use)g(an)f(HMM)g(model)f(for)h (the)g(global)f(motif)-182 3811 y(distrib)n(ution,)23 b(which)g(introduces)g(simple)h(dependencies)d(among)-182 3905 y(motif)34 b(instances)g(and)g(allo)n(ws)h(ef)n(\002cient)f(and)g (consistent)g(infer)n(-)-182 4000 y(ence)27 b(of)g(motif)g(locations.) 47 b(A)28 b(deterministic)e(algorithm,)i(v)n(aria-)-182 4095 y(tional)19 b(EM,)g(is)h(de)n(v)o(eloped)d(to)j(solv)o(e)f(the)h (comple)o(x)d(missing)j(v)n(alue)-182 4189 y(and)e(Bayesian)h(learning) e(problems)g(associated)i(with)g(our)f(model.)-182 4284 y(VEM)26 b(allo)n(ws)g(probabilistic)f(inference)f(in)i(the)g(local)g (alignment)-182 4379 y(and)f(the)h(global)f(distrib)n(ution)g(submodel) f(to)i(be)g(carried)f(out)g(vir)n(-)-182 4473 y(tually)d(separately)g (with)g(a)h(proper)e(Bayesian)i(interf)o(ace)f(connect-)-182 4568 y(ing)31 b(the)h(tw)o(o)h(processes.)60 b(This)32 b FL(divide)g(and)f(conquer)g FJ(strate)o(gy)-182 4662 y(mak)o(es)20 b(it)g(much)f(easier)i(to)f(de)n(v)o(elop)e(more)h (sophisticated)h(models)-182 4757 y(for)31 b(v)n(arious)h(aspects)h(of) f(motif)g(analysis)g(without)g(being)f(o)o(v)o(er)n(-)-182 4852 y(b)n(urdened)21 b(by)i(the)h(some)n(what)f(daunting)e(comple)o (xity)h(of)h(the)h(full)-182 4946 y(motif)19 b(problem.)-83 5041 y(As)32 b(discussed)e(at)i(length)e(in)h([22)n(],)j(the)d(HMDM)f (model)g(de-)-182 5136 y(scribes)44 b(a)h(rich)f(continuous)e(distrib)n (ution)i(of)g(PWMs)h(whose)-182 5230 y(position-speci\002c)26 b(parameters)h(follo)n(w)g(\002rst-order)f(Mark)o(o)o(v)g(de-)-182 5325 y(pendences,)e(and)g(which)h(are)f(not)h(captured)e(in)i(most)g (contempo-)1974 83 y(rary)i(motif)g(detection)g(algorithms.)46 b(Ne)n(v)o(ertheless,)29 b(although)c(it)1974 178 y(is)j(a)g(more)f(e)o (xpressi)n(v)o(e)f(model,)j(we)e(realize)h(that)g(the)f(actual)h(de-) 1974 272 y(pendencies)e(inside)h(the)h(motif)f(could)g(be)g(e)n(v)o(en) g(more)g(comple)o(x;)1974 367 y(further)17 b(in)m(v)o(estigations)f (into)i(these)h(properties)e(and)h(more)f(po)n(wer)n(-)1974 462 y(ful)26 b(models)f(are)h(needed.)41 b(Similarly)-5 b(,)27 b(the)f(HMM)g(global)f(model)1974 556 y(we)g(propose)d(is)k (only)d(a)i(\002rst)g(step)g(be)o(yond)d(the)j(con)m(v)o(entional)c(UI) 1974 651 y(model,)31 b(and)e(is)i(only)e(able)h(to)g(capture)f (dependencies)f(between)1974 746 y(motifs)34 b(and)g(motif)f(clusters)i (at)g(a)g(v)o(ery)e(limited)h(le)n(v)o(el)g(\(e.g.,)i(it)1974 840 y(can)19 b(not)h(model)e(higher)h(order)f(dependencies)f(such)j(as) g(hierarchi-)1974 935 y(cal)j(structures)f(and)h(long-distance)d (in\003uence)i(between)g(motifs\).)1974 1029 y(More)g(e)o(xpressi)n(v)o (e)f(models)h(are)g(needed)g(to)g(achie)n(v)o(e)g(these)h(goals.)1974 1124 y(Ne)n(v)o(ertheless,)35 b(under)d(the)h FK(LOGOS)g FJ(architecture,)h(e)o(xtensions)1974 1219 y(from)18 b(baseline)g(models)h(are)g(modular)e(and)h(the)h(probabilistic)f(cal-) 1974 1313 y(culations)37 b(in)m(v)n(olv)o(ed)g(can)h(also)g(be)g (handled)f(in)h(a)h FL(divide-and-)1974 1408 y(conquer)25 b FJ(f)o(ashion)g(via)h(generalized)f(v)n(ariational)g(inference.)41 b(W)-7 b(e)1974 1503 y(are)27 b(in)h(the)g(process)f(of)g(de)n(v)o (eloping)e(more)i(e)o(xpressi)n(v)o(e)f(v)o(ersions)1974 1597 y(of)18 b FK(LOGOS)p FJ(.)g(In)g(particular)m(,)f(recent)h(w)o (ork)g(by)g(Liu)g(et)h(al.)f([17)o(])h(and)1974 1692 y(Gupta)g(et)h(al.)g([9)o(])g(ha)n(v)o(e)f(moti)n(v)n(ated)g(us)h(to)f (pursue)g(combination)e(of)1974 1787 y(the)28 b(dictionary-based)e (models)h(with)i(our)f(approach)e(to)i(capture)1974 1881 y(richer)e(motif)g(properties)f(in)i(comple)o(x)e(sequences.)43 b(W)-7 b(e)28 b(are)f(op-)1974 1976 y(timistic)22 b(that)g FK(LOGOS)f FJ(can)g(serv)o(e)g(as)i(a)f(\003e)o(xible)e(frame)n(w)o (ork)g(for)1974 2071 y(motif)g(analysis)g(in)g(biopolymer)e(sequences.) 1974 2284 y FM(Ackno)o(wledgments)2073 2482 y FJ(W)-7 b(e)21 b(thank)d(Prof.)24 b(Michael)18 b(Eisen)i(for)e(helpful)g (discussions)h(on)1974 2577 y(motif)h(structures.)1974 2791 y FM(Refer)n(ences)2025 2981 y Fc([1])42 b(T)-6 b(.)14 b(L.)g(Baile)o(y)h(and)g(C.)f(Elkan.)19 b(Unsupervised)d (learning)g(of)e(multiple)2154 3067 y(motifs)h(in)h(biopolymers)h (using)f(EM.)k Fa(Mac)o(hine)c(Learning)p Fc(,)h(21:51\226)2154 3154 y(80,)i(1995.)2025 3230 y([2])42 b(B.)25 b(P)-8 b(.)26 b(Berman,)i(Y)-10 b(.)26 b(Nib)o(u,)i(B.)e(D.)f(Pfeif)n(fer)m(,) i(P)-8 b(.)26 b(T)-6 b(omancak,)29 b(S.)c(E.)2154 3317 y(Celnik)o(er)m(,)j(M.)f(Le)n(vine,)h(G.)e(M.)h(Rubin,)h(and)f(M.)g(B.) f(Eisen.)51 b(Ex-)2154 3404 y(ploiting)24 b(transcription)h(f)o(actor)f (binding)h(site)f(clustering)g(to)g(iden-)2154 3491 y(tify)c(cis-re)o (gulatory)h(modules)h(in)m(v)o(olv)o(ed)g(in)e(pattern)h(formation)g (in)2154 3577 y(the)15 b(Drosophila)g(genome.)k Fa(Pr)m(oc.)14 b(Natl.)g(Acad.)h(Sci.)g(USA)p Fc(,)f(99:757\226)2154 3664 y(762,)19 b(2002.)2025 3740 y([3])42 b(H.)20 b(Bussemak)o(er)m(,)i (H.)e(Li,)h(and)g(E.)f(Siggia.)33 b(Building)21 b(a)g(dictionary)2154 3827 y(for)i(genomes:)34 b(Identi\002cation)24 b(of)g(presumpti)n(v)o (e)g(re)o(gulatory)h(sites)2154 3914 y(by)18 b(statistical)f(analysis.) 25 b Fa(Pr)m(oc.)17 b(Natl.)g(Acad.)h(Sci.)f(USA)p Fc(,)g(97,)h(2000.) 2025 3990 y([4])42 b(E.)24 b(H.)g(Da)o(vidson.)47 b Fa(Genomic)25 b(Re)m(gulatory)h(Systems)p Fc(.)47 b(Academic)2154 4077 y(Press,)18 b(2001.)2025 4153 y([5])42 b(B.)26 b(Efron.)54 b(Empirical)27 b(Bayes)h(methods)g(for)f(combining)i(lik)o(eli-)2154 4240 y(hoods)f(\(with)e(discussion\).)53 b Fa(J)n(.)27 b(Amer)-8 b(.)25 b(Statist.)h(Assoc.)p Fc(,)j(91:538\226)2154 4326 y(565,)19 b(1996.)2025 4403 y([6])42 b(M.)20 b(Eisen.)30 b(Structural)19 b(properties)i(of)f(transcription)g(f)o(actor)o(-DN)m (A)2154 4489 y(interactions)j(and)h(the)f(inference)h(of)f(sequence)i (speci\002city)-5 b(.)40 b(sub-)2154 4576 y(mitted,)18 b(2003.)2025 4652 y([7])42 b(M.)27 b(C.)g(Frith,)h(U.)f(Hansen,)k(and)d (Z.)e(W)-6 b(eng.)55 b(Detection)28 b(of)f(cis)h(-)2154 4739 y(element)19 b(clusters)f(in)h(higher)g(eukaryotic)h(DN)m(A.)27 b Fa(Bioinformatics)p Fc(,)2154 4826 y(17:878\226889,)21 b(2001.)2025 4902 y([8])42 b(D.)18 b(GuhaThakurta)j(and)e(G.)g(D.)f (Stormo.)27 b(Identifying)20 b(tar)o(get)f(sites)2154 4989 y(for)k(cooperati)n(v)o(ely)h(binding)g(f)o(actors.)41 b Fa(Bioinform.)p Fc(,)23 b(17:608\226621,)2154 5075 y(2001.)2025 5151 y([9])42 b(M.)19 b(Gupta)h(and)g(J.)g(Liu.)28 b(Disco)o(v)o(ery)20 b(of)g(conserv)o(ed)h(sequence)g(pat-)2154 5238 y(terns)j(using)i(a)f(stochastic)g(dictionary)h(model.)46 b Fa(J)n(.)24 b(Amer)-8 b(.)24 b(Statist.)2154 5325 y(Assoc.)p Fc(,)18 b(98,)h(2003.)p eop %%Page: 11 11 11 10 bop -169 83 a Fc([10])42 b(J.)27 b(V)-10 b(.)27 b(Helden,)j(A.)c(Rios,)j(and)f(J.)f(Collado-V)l(ides.)53 b(Disco)o(v)o(ering)-3 170 y(re)o(gulatory)21 b(elements)g(in)e (non-coding)j(sequences)g(by)f(analysis)f(of)-3 257 y(spaced)g(dyads.) 28 b Fa(Nucleic)19 b(Acids)g(Res.)p Fc(,)f(28:1808\2261818,)k(2000.) -169 339 y([11])42 b(G.)18 b(Z.)f(Hertz)g(and)i(G.)e(D.)g(Stormo.)25 b(Identifying)18 b(DN)m(A)g(and)h(protein)-3 426 y(patterns)j(with)g (statistically)e(signi\002cant)i(alignments)h(of)e(multiple)-3 513 y(sequences.)29 b Fa(Bioinform.)p Fc(,)18 b(15:563\226577,)j(1999.) -169 595 y([12])42 b(J.)23 b(D.)g(Hughes,)h(P)-8 b(.)22 b(W)-7 b(.)23 b(Estep,)g(S.)f(T)-6 b(a)o(v)n(azoie,)24 b(and)g(G.)f(M.)g(Church.)-3 682 y(Computational)j(identi\002cation)f (of)f(cis-re)o(gulatory)h(elements)g(as-)-3 769 y(sociated)k(with)e (groups)i(of)f(functionally)g(related)g(genes)h(in)f(Sac-)-3 856 y(charomyces)20 b(cere)n(visiae.)26 b Fa(J)n(.)18 b(Mol.)g(Biol)p Fc(,)g(296\(5\):1205\22614,)j(2000.)-169 938 y([13])42 b(M.)18 b(I.)f(Jordan,)i(Z.)e(Ghahramani,)i(T)-6 b(.)18 b(S.)f(Jaakk)o(ola,)i(and)f(L.)f(K.)h(Saul.)-3 1025 y(An)e(introduction)g(to)f(v)n(ariational)g(methods)h(for)f (graphical)h(models.)-3 1112 y(In)k(M.)g(I.)f(Jordan,)i(editor)m(,)e Fa(Learning)i(in)f(Gr)o(aphical)g(Models)p Fc(.)g(MIT)-3 1198 y(Press,)f(Cambridge,)g(1999.)-169 1281 y([14])42 b(K.)24 b(K)n(echris,)h(E.)e(v)n(an)i(Zwet,)g(P)-8 b(.)22 b(Bick)o(el,)k(and)e(M.)g(Eisen.)43 b(Detect-)-3 1368 y(ing)16 b(DN)m(A)f(re)o(gulatory)i(motifs)e(by)h(incoporating)g (position-speci\002c)-3 1455 y(base)k(conserv)n(ation.)28 b Fa(submitted)p Fc(,)19 b(2003.)-169 1537 y([15])42 b(J.)21 b(Liu,)h(X.)f(Liu,)g(and)i(D.)e(Brutlag.)35 b(Bioprospector:)29 b(Disco)o(v)o(ering)-3 1624 y(conserv)o(ed)18 b(DN)m(A)d(motifs)g(in)h (upstream)g(re)o(gulatory)g(re)o(gions)g(of)g(co-)-3 1711 y(e)o(xpressed)21 b(genes.)27 b(In)19 b Fa(Pr)m(oc.of)g(PSB)p Fc(,)f(2001.)-169 1793 y([16])42 b(J.)30 b(Liu,)j(A.)c(Neuw)o(ald,)34 b(and)d(C.)f(La)o(wrence.)63 b(Bayesian)31 b(models)-3 1880 y(for)25 b(multiple)g(local)h(sequence)g(alignment)g(and)g(Gibbs)f (sampling)-3 1967 y(strate)o(gies.)i Fa(J)n(.)19 b(Amer)-8 b(.)18 b(Statist.)g(Assoc)p Fc(,)h(90:1156\2261169,)j(1995.)-169 2049 y([17])42 b(X.)26 b(S.)g(Liu,)i(D.)e(L.)g(Brutlag,)i(and)f(J.)g (S.)e(Liu.)51 b(An)27 b(algorithm)g(for)-3 2136 y(\002nding)17 b(protein-DN)m(A)g(binding)g(sites)e(with)h(applications)h(to)f(chro-) -3 2223 y(matin)34 b(immunoprecipitation)h(microarray)f(e)o (xperiments.)74 b Fa(Nat)-3 2310 y(Biotec)o(hnol)p Fc(,)19 b(20\(8\):835\2269,)i(2002.)-169 2392 y([18])42 b(L.)24 b(A.)f(Pennacchio)j(and)f(E.)e(M.)h(Rubin.)44 b(Genomic)25 b(strate)o(gies)f(to)-3 2479 y(identify)f(mammalian)h(re)o(gulatory)f (sequences.)40 b Fa(Natur)m(e)24 b(Re)o(vie)o(ws)-3 2566 y(Genetics)p Fc(,)19 b(2\(2\):100\226109,)i(2001.)-169 2648 y([19])42 b(T)-6 b(.)28 b(D.)e(Schneider)i(and)h(R.)d(M.)i (Stephens.)55 b(Sequence)28 b(logos:)41 b(A)-3 2735 y(ne)n(w)21 b(w)o(ay)g(to)f(display)h(consensus)i(sequences.)33 b Fa(Nucl.)20 b(Acids)g(Res.)p Fc(,)-3 2822 y(18:6097\2266100,)j(1990.) -169 2905 y([20])42 b(G.)21 b(D.)f(Stormo)h(and)h(D.)f(S.)f(Fields.)33 b(Speci\002city)-5 b(,)21 b(free)g(ener)o(gy)g(and)-3 2991 y(information)h(content)f(in)g(protein-DN)m(A)h(interactions.)33 b Fa(T)l(r)m(ends)21 b(in)-3 3078 y(Bioc)o(hemical)f(Sciences)p Fc(,)f(23:109\226113,)i(1998.)-169 3161 y([21])42 b(L.)23 b(Stryer)l(.)40 b Fa(Bioc)o(hemistry)23 b(\(4th.)g(edition\))p Fc(.)41 b(W)-7 b(.)22 b(H.)h(Freeman)g(and)-3 3247 y(Compan)o(y)-5 b(,)20 b(1995.)-169 3330 y([22])42 b(E.)21 b(P)-8 b(.)20 b(Xing,)i(M.)g(I.)f(Jordan,)h(R.)f(M.)h(Karp,)f(and)i(S.)d(Russell.)35 b(A)21 b(hi-)-3 3417 y(erarchical)d(Bayesian)g(Mark)o(o)o(vian)h(model) e(for)g(motifs)g(in)g(biopoly-)-3 3504 y(mer)j(sequences.)30 b(In)19 b Fa(Pr)m(oc.)g(of)g(Advances)h(in)g(Neur)o(al)f(Information)-3 3590 y(Pr)m(ocessing)h(Systems)f(16)p Fc(,)g(2003.)-169 3673 y([23])42 b(E.)17 b(P)-8 b(.)15 b(Xing,)i(M.)g(I.)g(Jordan,)h(and) f(S.)f(Russell.)23 b(A)16 b(generalized)j(mean)-3 3760 y(\002eld)h(algorithm)g(for)g(v)n(ariational)g(inference)g(in)g(e)o (xponential)h(f)o(am-)-3 3846 y(ilies.)28 b(In)20 b Fa(Pr)m(oceedings)g (of)g(the)f(19th)h(Annual)g(Confer)m(ence)h(on)f(Un-)-3 3933 y(certainty)g(in)f(AI)p Fc(,)e(2003.)p eop %%Trailer end userdict /end-hook known{end-hook}if %%EOF