Computer Applications in the Biosciences, Volume 12 (original) (raw)

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Volume 12, Number 1, February 1996

Articles

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    Giorgio Grillo, Marcella Attimonelli, Sabino Liuni, Graziano Pesole:
    CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. 1-8
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    Malcolm F. Wilkins, Lynne Boddy, Colin W. Morris, Richard Jonker:
    A comparison of some neural and non-neural methods for identification of phytoplankton from flow cytometry data. 9-18
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    Sridhar Hannenhalli, William Feldman, Herbert F. Lewis, Steven Skiena, Pavel A. Pevzner:
    Positional sequencing by hybridization. 19-24
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    Eugene S. Carter II, C. S. Tung:
    NAMOT2 - a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures. 25-30
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    Xiaojun Guan, Edward C. Uberbacher:
    Alignments of DNA and protein sequences containing frameshift errors. 31-40
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    Piero Fariselli, Rita Casadio:
    HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins. 41-48
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    Vsevolod J. Makeev, Vladimir G. Tumanyan:
    Search of periodicities in primary structure of biopolymers: a general Fourier approach. 49-54
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    A. Nandy:
    Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences. 55-62
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    Guy Perrière, Jean Thioulouse:
    On-line tools for sequence retrieval and multivariate statistics in molecular biology. 63-69
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    Franz Wolfertstetter, Kornelie Frech, Grit Herrmann, Thomas Werner:
    Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. 71-80

Volume 12, Number 2, April 1996

Articles

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    Carlo Caporale, Ciro Sepe, Carla Caruso, Anna M. Garzillo, Vincenzo Buonocore:
    An algorithm to analyse the hydrolysis pathway of peptides and proteins by sequence analyses of unfractionated digestion mixtures. 81-88
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    D. N. Perkins, Terri K. Attwood:
    XFINGER: a tool for searching and visualising protein fingerprints and patterns. 89-94
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    Richard Hughey, Anders Krogh:
    Hidden Markov models for sequence analysis: extension and analysis of the basic method. 95-107
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    Cathy H. Wu, Sheng Zhao, Hsi-Lien Chen, Chin-Ju Lo, Jerry McLarty:
    Motif identification neural design for rapid and sensitive protein family search. 109-118
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    Wolfgang Vahrson, Klaus Hermann, Jürgen Kleffe, Burghardt Wittig:
    Object-oriented sequence analysis: SCL - a C++ class library. 119-127
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    F. Eggenberger, Nicole Redaschi, Reinhard Doelz:
    FastAlert - an automatic search system to alert about new entries in biological sequence databanks. 129-133
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    Jorja G. Henikoff, Steven Henikoff:
    Using substitution probabilities to improve position-specific scoring matrices. 135-143
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    D. Curtis Jamison, Brad Mills, Bruce R. Schatz:
    An extensible network query unification system for biological databases. 145-150
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    G. Schaftenaar, K. Cuelenaere, Jan H. Noordik, Thure Etzold:
    A Tcl-based SRS v.4 interface. 151-155
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    Dan S. Prestridge:
    SIGNAL SCAN 4.0: additional databases and sequence formats. 157-160

Volume 12, Number 3, June 1996

Articles

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    Igor B. Rogozin, Luciano Milanesi, Nikolay A. Kolchanov:
    Gene structure prediction using information on homologous protein sequence. 161-170
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    Bruce A. Shapiro, Jin Chu Wu:
    An annealing mutation operator in the genetic algorithms for RNA folding. 171-180
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    A. S. Law, D. W. Burt:
    qValue - a program to calculate comparative measures of genomic reorganisation from cytogenetic and/or linkage information. 181-183
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    John A. Byers:
    TAXOKEY: a universal taxonomic key program using DOS text files and graphics. 185-189
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    Raj K. Singh, D. L. Hoffman, Stephen G. Tell, C. Thomas White:
    BioSCAN: a network sharable computational resource for searching biosequence databases. 191-196
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    Grit Herrmann, Astrid Schön, R. Brack-Werner, Thomas Werner:
    CONRAD: a method for identification of variable and conserved regions within proteins by scale-space filtering. 197-203
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    Akihiro Nakaya, Kenjiro Taura, Kenji Yamamoto, Akinori Yonezawa:
    Visualization of RNA secondary structures using highly parallel computers. 205-211
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    Shigehiko Kanaya, Yoshihiro Kudo, Yasukazu Nakamura, Toshimichi Ikemura:
    Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage. 213-225
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    Jürgen Sühnel:
    Image library of biological macromolecules. 227-229
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    Y. Wada, H. Yasue:
    Development of an animal genome database and its search system. 231-235
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    Kirill Degtyarenko, Péter Fábián:
    The directory of P450-containing systems on WorldWide Web. 237-240
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    Jean-Paul Rolland, Mohamed J. Flifla, Mireille Garreau, Daniel Thomas:
    IBIS version 3: an OSF/Motif-based interface for IBIS - integrated biological imaging system. 241-245
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    O. Matzura, A. Wennborg:
    RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. 247-249
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    Ross D. King, C. G. Angus:
    PM - protein music. 251-252
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    Vitali Proutski, Edward C. Holmes:
    Primer Master: a new program for the design and analysis of PCR primers. 253-255
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    B. I. Osborne:
    Three sets of Macintosh AppleScripts for the automatic submission of sequence data to the internet BLAST server. 257-258

Volume 12, Number 4, August 1996

Articles

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    Jin Kim, James R. Cole, Sakti Pramanik:
    Alignment of possible secondary structures in multiple RNA sequences using simulated annealing. 259-267
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    Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan P. Arnold:
    PARODS - a study of parallel algorithms for ordering DNA sequences. 269-280
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    Klaus Lindauer, Cezar Bendic, Jürgen Sühnel:
    HBexplore - a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules. 281-289
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    Ingrid B. Jakobsen, Simon Easteal:
    A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. 291-295
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    Igor Kuznetsov, Pavel Morozov:
    GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space. 297-301
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    William Noble Grundy, Timothy L. Bailey, Charles Elkan:
    ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. 303-310
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    Lijuan Hu, Elaine F. Saulinskas, Peter Johnson, Peter de B. Harrington:
    Development of an expert system for amino acid sequence identification. 311-318
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    Cheng Che Chen, Richard O. Chen, Russ B. Altman:
    Constraining volume by matching the moments of a distance distribution. 319-326
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    Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler:
    Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. 327-345
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    Joël-Paul Grillasca, Denis Aubert, Richard Planells, N. Domingo, H. Lafont:
    LITTLE KEVIN: a program for the estimation of protein homology by analysing the amino acid compositions and sequences. 347-351
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    M. P. Maradona:
    Software for microbial fingerprinting by means of the infrared spectra. 353-356
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    Roderic D. M. Page:
    TreeView: an application to display phylogenetic trees on personal computers. 357-358

Volume 12, Number 5, October 1996

Articles

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    Philipp Bucher, James W. Fickett, Artemis G. Hatzigeorgiou:
    Computational analysis of transcriptional regulatory elements: a field in flux. 361-362
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    C. Fondrat, A. Kalogeropoulos:
    Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III. 363-374
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    Craig J. Benham:
    Computation of DNA structural variability - a new predictor of DNA regulatory regions. 375-381
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    Alexander Bolshoy, I. Ioshikhes, Edward N. Trifonov:
    Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case. 383-389
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    Gordon B. Hutchinson:
    The prediction of vertebrate promoter regions using differential hexamer frequency analysis. 391-398
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    Luciano Milanesi, Marco Muselli, P. Arrigo:
    Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes. 399-404
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    Kerstin Quandt, Korbinian Grote, Thomas Werner:
    GenomeInspector: a new approach to detect correlation patterns of elements on genomic sequences. 405-413
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    David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides:
    Syntactic recognition of regulatory regions in Escherichia coli. 415-422
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    Edward N. Trifonov:
    Interfering contexts of regulatory sequence elements. 423-429
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    Jean-Michel Claverie, Stéphane Audic:
    The statistical significance of nucleotide position-weight matrix matches. 431-439
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    Holger Karas, Rainer Knüppel, Wolfgang Schulz, Heinz Sklenar, Edgar Wingender:
    Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements. 441-446

Volume 12, Number 6, December 1996

Articles

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    Jens Hanke, Jens G. Reich:
    Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures. 447-454
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    Frédéric Hospital, Christine Dillmann, A. E. Melchinger:
    A general algorithm to compute multilocus genotype frequencies under various mating systems. 455-462
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    Gilles Labesse:
    MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis. 463-467
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    Andrew Rambaut, Nicholas C. Grassly, Sean Nee, Paul H. Harvey:
    Bi-De: an application for simulating phylogenetic processes. 469-471
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    Richard Hughey:
    Parallel hardware for sequence comparison and alignment. 473-479
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    Joel Wallman, Guy A. Hoelzer, Don J. Melnick:
    The effects of social structure, geographical structure, and population size on the evolution of mitochondrial DNA: I. A simulation model. 481-489
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    U. S. Murty, K. Jamil, D. Krishna, P. J. Reddy:
    Rule-based system for the fast identification of species of Indian Anopheline mosquitoes. 491-495
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    X. Huang, J. Zhang:
    Methods for comparing a DNA sequence with a protein sequence. 497-506
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    Laurent Duret, Elisabeth Gasteiger, Guy Perrière:
    LALNVIEW: a graphical viewer for pairwise sequence alignments. 507-510
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    Ying Xu, Edward C. Uberbacher:
    A polynomial-time algorithm for a class of protein threading problems. 511-517
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    Guy Perrière, J. R. Lobry, Jean Thioulouse:
    Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acid sequences. 519-524
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    Rob W. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend:
    The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. 525-529
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    Salvatore Lanzavecchia, L. Tosoni, Pier Luigi Bellon:
    Fast sinogram computation and the sinogram-based alignment of images. 531-537
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    W. J. Heitler:
    A simple method for the removal of mains interference from pre-recorded electrophysiological data. 539-542
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    Nicolas Galtier, Manolo Gouy, Christian Gautier:
    SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. 543-548
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    L. Tosoni, Salvatore Lanzavecchia, Pier Luigi Bellon:
    Image and volume data rotation with 1- and 3-pass algorithms. 549-552
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    Jadranka Lazovic:
    Selection of amino acid parameters for Fourier transform-based analysis of proteins. 553-562

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