Comparative genomics: genome-wide analysis in metazoan eukaryotes (original) (raw)

• The C. elegans Genome Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018 (1998).
• Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185–2195 (2000).
  PubMed Google Scholar
• Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
  CAS PubMed Google Scholar
• Venter, J. C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).
  Article CAS PubMed Google Scholar
• Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301–1310 (2002).
  CAS PubMed Google Scholar
• Holt, R. A. et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298, 129–149 (2002).
  CAS PubMed Google Scholar
• Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002). The first whole-genome comparative analysis of two mammalian organisms.
  CAS PubMed Google Scholar
• Dehal, P. et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298, 2157–2167 (2002). References 1–8 are the original publications for some of the sequenced 'entire' metazoan genomes.
  CAS PubMed Google Scholar
• Bolshakov, V. N. et al. A comparative genomic analysis of two distant diptera, the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae. Genome Res. 12, 57–66 (2002).
  CAS PubMed PubMed Central Google Scholar
• Zdobnov, E. M. et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298, 149–159 (2002). One of three papers about the Anopheles genome, which gives a good flavour of more distant comparative genomics compared with the inter-mammal papers.
  CAS PubMed Google Scholar
• Dehal, P. et al. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. Science 293, 104–111 (2001).
  CAS PubMed Google Scholar
• Mural, R. J. et al. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296, 1661–1671 (2002).
  CAS PubMed Google Scholar
• Hedges, S. B. The origin and evolution of model organisms. Nature Rev. Genet. 3, 838–849 (2002).
  CAS PubMed Google Scholar
• Graur, D. & Wen-Hsiung, L. Fundamentals of Molecular Evolution (Sinauer Associates, Inc., Sunderland, Massachusetts, 2000).
  Google Scholar
• Goff, S. A. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92–100 (2002).
  CAS PubMed Google Scholar
• Freeling, M. Grasses as a single genetic system: reassessment 2001. Plant Physiol. 125, 1191–1197 (2001).
  CAS PubMed PubMed Central Google Scholar
• Van Sluys, M. A. et al. Comparative genomic analysis of plant-associated bacteria. Annu. Rev. Phytopath. 40, 169–189 (2002).
  CAS Google Scholar
• Edwards, R. A., Olsen, G. J. & Maloy, S. R. Comparative genomics of closely related salmonellae. Trends Microbiol. 10, 94–99 (2002).
  CAS PubMed Google Scholar
• Brosch, R., Pym, A. S., Gordon, S. V. & Cole, S. T. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 9, 452–458 (2001).
  CAS PubMed Google Scholar
• Paulsen, I. T., Chen, J., Nelson, K. E. & Saier, M. H. Comparative genomics of microbial drug efflux systems. J. Mol. Microbiol. Biotech. 3, 145–150 (2001).
  CAS Google Scholar
• McClelland, M. et al. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res. 28, 4974–4986 (2000).
  CAS PubMed PubMed Central Google Scholar
• Kimura, M. Evolutionary rate at the molecular level. Nature 217, 624–626 (1968).
  CAS PubMed Google Scholar
• King, J. L. & Jukes, T. H. Non-Darwinian evolution. Science 164, 788–798 (1969).
  CAS PubMed Google Scholar
• Ohta, T. & Tachida, H. Theoretical study of near neutrality. I. Heterozygosity and rate of mutant substitution. Genetics 126, 219–229 (1990).
  CAS PubMed PubMed Central Google Scholar
• Miller, W. Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics 17, 391–397 (2001).
  CAS PubMed Google Scholar
• Smith, T. F. & Waterman, M. S. Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197 (1981).
  CAS PubMed Google Scholar
• Needleman, S. B. & Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970).
  CAS PubMed Google Scholar
• Mayor, C. et al. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16, 1046–1047 (2000).
  Article CAS PubMed Google Scholar
• Harris, T. W. et al. WormBase: a cross-species database for comparative genomics. Nucleic Acids Res. 31, 133–137 (2003).
  CAS PubMed PubMed Central Google Scholar
• Clamp, M. et al. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res. 31, 38–42 (2003).
  CAS PubMed PubMed Central Google Scholar
• Karolchik, D. et al. The UCSC genome browser database. Nucleic Acids Res. 31, 51–54 (2003).
  CAS PubMed PubMed Central Google Scholar
• Giardine, B. et al. GALA: a database for genomic sequence alignments and annotations. Genome Res. (in the press).
• Pennacchio, L. A. et al. An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science 294, 169–173 (2001).
  CAS PubMed Google Scholar
• Wasserman, W. W., Palumbo, M., Thompson, W., Fickett, J. W. & Lawrence, C. E. Human–mouse genome comparisons to locate regulatory sites. Nature Genet. 26, 225–228 (2000).
  CAS PubMed Google Scholar
• Jareborg, N., Birney, E. & Durbin, R. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res. 9, 815–824 (1999).
  CAS PubMed PubMed Central Google Scholar
• Roest Crollius, H. et al. Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nature Genet. 25, 235–238 (2000). The first large-scale comparison between two vertebrate genomes.
  CAS PubMed Google Scholar
• Gilligan, P., Brenner, S. & Venkatesh, B. Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences. Gene 294, 35–44 (2002).
  CAS PubMed Google Scholar
• Kent, W. J. & Zahler, A. M. Conservation, regulation, synteny, and introns in a large-scale C. briggsae_–_C. elegans genomic alignment. Genome Res. 10, 1115–1125 (2000). The first software implementation of a pair-HMM to align sequences.
  CAS PubMed Google Scholar
• Delcher, A. L. et al. Alignment of whole genomes. Nucleic Acids Res. 27, 2369–2376 (1999).
  CAS PubMed PubMed Central Google Scholar
• Delcher, A. L., Phillippy, A., Carlton, J. & Salzberg, S. L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478–2483 (2002).
  PubMed PubMed Central Google Scholar
• Ma, B., Tromp, J. & Li, M. PatternHunter: faster and more sensitive homology search. Bioinformatics 18, 440–445 (2002). The publication that proposed the original two weighted-spaced model to identify nearly exact matching words
  CAS PubMed Google Scholar
• Batzoglou, S., Pachter, L., Mesirov, J. P., Berger, B. & Lander, E. S. Human and mouse gene structure: comparative analysis and application to exon prediction. Genome Res. 10, 950–958 (2000).
  CAS PubMed PubMed Central Google Scholar
• Mullikin, J. C. & Ning, Z. The phusion assembler. Genome Res. 13, 81–90 (2003).
  CAS PubMed PubMed Central Google Scholar
• Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• Schwartz, S. et al. Human–mouse alignments with BLASTZ. Genome Res. 13, 103–107 (2003).
  CAS PubMed PubMed Central Google Scholar
• Chiaromonte, F., Yap, V. B. & Miller, W. Scoring pairwise genomic sequence alignments. Pac. Symp. Biocomput. 115–126 (2002).
• Kent, W. J. BLAT — the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
  CAS PubMed PubMed Central Google Scholar
• Bray, N., Dubchak, I. & Pachter, L. AVID: a global alignment program. Genome Res. 13, 97–102 (2003).
  CAS PubMed PubMed Central Google Scholar
• Couronne, O. et al. Strategies and tools for whole genome alignments. Genome Res. 13, 73–80 (2003).
  CAS PubMed PubMed Central Google Scholar
• Brudno, M. et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. (in the press).
• Schwartz, S. et al. PipMaker — a web server for aligning two genomic DNA sequences. Genome Res. 10, 577–586 (2000).
  CAS PubMed PubMed Central Google Scholar
• Elnitski, L. et al. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics 80, 681–690 (2002).
  CAS PubMed Google Scholar
• Durbin, R., Eddy, S., Krogh, A. & Mitchison, G. in Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids 80–99 (Cambridge Univ. Press, Cambridge, UK, 1998).
  Google Scholar
• Chiaromonte, F. et al. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proc. Natl Acad. Sci USA 98, 14503–14508 (2001).
  CAS PubMed PubMed Central Google Scholar
• Zhang, M. Q. Computational prediction of eukaryotic protein-coding genes. Nature Rev. Genet 3, 698–709 (2002).
  CAS PubMed Google Scholar
• Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997).
  CAS PubMed Google Scholar
• Alexandersson, M., Cawley, S. & Pachter, L. SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res. (in the press). The most complete pair-HMM model for gene prediction that has been implemented so far.
• Pachter, L., Alexandersson, M. & Cawley, S. Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comput. Biol. 9, 389–399 (2002).
  CAS PubMed Google Scholar
• Meyer, I. M. & Durbin, R. Comparative ab initio prediction of gene structures using pair-HMMs. Bioinformatics 18, 1309–1318 (2002).
  CAS PubMed Google Scholar
• Korf, I., Flicek, P., Duan, D. & Brent, M. R. Integrating genomic homology into gene structure prediction. Bioinformatics 17 (Suppl.) S140–S148 (2001). This paper describes Twinscan, which is one of the best informant-HMM gene-modelling approaches.
  PubMed Google Scholar
• Wiehe, T., Gebauer-Jung, S., Mitchell-Olds, T. & Guigo, R. SGP-1: prediction and validation of homologous genes based on sequence alignments. Genome Res. 11, 1574–1583 (2001).
  CAS PubMed PubMed Central Google Scholar
• Yeh, R. F., Lim, L. P. & Burge, C. B. Computational inference of homologous gene structures in the human genome. Genome Res. 11, 803–816 (2001).
  CAS PubMed PubMed Central Google Scholar
• Tagle, D. A. et al. Embryonic ε- and γ-globin genes of a prosimian primate (Galago crassicaudatus): nucleotide and amino-acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203, 439–455 (1988).
  CAS PubMed Google Scholar
• Levy, S., Hannenhalli, S. & Workman, C. Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics 17, 871–877 (2001).
  CAS PubMed Google Scholar
• Fickett, J. W. & Wasserman, W. W. Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol. 11, 19–24 (2000).
  CAS PubMed Google Scholar
• Aparicio, S. et al. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl Acad. Sci. USA 92, 1684–1688 (1995).
  CAS PubMed PubMed Central Google Scholar
• Flint, J. et al. Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the α-globin cluster. Hum. Mol. Genet. 10, 371–382 (2001).
  CAS PubMed Google Scholar
• Webb, C. T., Shabalina, S. A., Ogurtsov, A. Y. & Kondrashov, A. S. Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae. Nucleic Acids Res. 30, 1233–1239 (2002).
  CAS PubMed PubMed Central Google Scholar
• Dieterich, C. et al. Annotating regulatory DNA based on man–mouse genomic comparison. Bioinformatics 18 (Suppl.), S84–S90 (2002).
  PubMed Google Scholar
• Praz, V., Perier, R., Bonnard, C. & Bucher, P. The eukaryotic promoter database, EPD: new entry types and links to gene expression data. Nucleic Acids Res. 30, 322–324 (2002).
  CAS PubMed PubMed Central Google Scholar
• Hamdi, H. K., Nishio, H., Tavis, J., Zielinski, R. & Dugaiczyk, A. Alu-mediated phylogenetic novelties in gene regulation and development. J. Mol. Biol. 299, 931–939 (2000).
  CAS PubMed Google Scholar
• Liu, T., Wu, J. & He, F. Evolution of _cis_-acting elements in 5′ flanking regions of vertebrate actin genes. J. Mol. Evol. 50, 22–30 (2000).
  CAS PubMed Google Scholar
• Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1545 (1999).
  CAS PubMed PubMed Central Google Scholar
• Dermitzakis, E. T. & Clark, A. G. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19, 1114–1121 (2002). The authors estimate that ∼30–40% of the functional cis -acting elements in human are not functional in rodents.
  CAS PubMed Google Scholar
• Ludwig, M. Z., Bergman, C., Patel, N. H. & Kreitman, M. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403, 564–567 (2000). A publication that studies the compensatory mutation and stabilizing selection of cis -acting elements in two species of Drosophila.
  CAS PubMed Google Scholar
• Elnitski, L. et al. Distinguishing regulatory DNA from neutral sites. Genome Res. 13, 64–72 (2003).
  CAS PubMed PubMed Central Google Scholar
• Bailey, T. L. & Elkan, C. The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3, 21–29 (1995).
  CAS PubMed Google Scholar
• Roth, F. P., Hughes, J. D., Estep, P. W. & Church, G. M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnol. 16, 939–945 (1998).
  CAS Google Scholar
• Morgenstern, B., Frech, K., Dress, A. & Werner, T. DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14, 290–294 (1998).
  CAS PubMed Google Scholar
• Hertz, G. Z. & Stormo, G. D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15, 563–577 (1999).
  CAS PubMed Google Scholar
• Brazma, A., Jonassen, I., Vilo, J. & Ukkonen, E. Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 8, 1202–1215 (1998).
  CAS PubMed PubMed Central Google Scholar
• Hughes, J. D., Estep, P. W., Tavazoie, S. & Church, G. M. Computational identification of _cis_-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296, 1205–1214 (2000).
  CAS PubMed Google Scholar
• Blanchette, M. & Tompa, M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12, 739–748 (2002).
  CAS PubMed PubMed Central Google Scholar
• Gottgens, B. et al. Transcriptional regulation of the stem cell leukemia gene (SCL) —comparative analysis of five vertebrate SCL loci. Genome Res. 12, 749–759 (2002).
  CAS PubMed PubMed Central Google Scholar
• Loots, G. G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288, 136–140 (2000).
  CAS PubMed Google Scholar
• Dubchak, I. et al. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 10, 1304–1306 (2000).
  CAS PubMed PubMed Central Google Scholar
• Zhu, J., Liu, J. S. & Lawrence, C. E. Bayesian adaptive sequence alignment algorithms. Bioinformatics 14, 25–39 (1998).
  CAS PubMed Google Scholar
• Berman, B. P. et al. Exploiting transcription factor binding site clustering to identify _cis_-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA 99, 757–762 (2002).
  CAS PubMed PubMed Central Google Scholar
• Levy, S. & Hannenhalli, S. Identification of transcription factor binding sites in the human genome sequence. Mamm. Genome 13, 510–514 (2002).
  CAS PubMed Google Scholar
• Chao, K. M., Hardison, R. C. & Miller, W. Recent developments in linear-space alignment methods: a survey. J. Comput. Biol. 1, 271–291 (1994).
  CAS PubMed Google Scholar
• Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994).
  CAS PubMed PubMed Central Google Scholar
• Corpet, F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16, 10881–10890 (1988).
  CAS PubMed PubMed Central Google Scholar
• Stojanovic, N. et al. Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Res. 27, 3899–3910 (1999).
  CAS PubMed PubMed Central Google Scholar
• Wingender, E. et al. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 28, 316–319 (2000).
  CAS PubMed PubMed Central Google Scholar
• Quandt, K., Frech, K., Karas, H., Wingender, E. & Werner, T. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 23, 4878–4884 (1995).
  CAS PubMed PubMed Central Google Scholar
• Jegga, A. G. et al. Detection and visualization of compositionally similar _cis_-regulatory element clusters in orthologous and coordinately controlled genes. Genome Res. 12, 1408–1417 (2002).
  CAS PubMed PubMed Central Google Scholar
• Loots, G. G., Ovcharenko, I., Pachter, L., Dubchak, I. & Rubin, E. M. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 12, 832–839 (2002).
  PubMed PubMed Central Google Scholar
• Hedges, S. B. & Kumar, S. Genomics: vertebrate genomes compared. Science 297, 1283–1285 (2002).
  CAS PubMed Google Scholar
• Venkatesh, B., Gilligan, P. & Brenner, S. Fugu: a compact vertebrate reference genome. FEBS Lett. 476, 3–7 (2000).
  CAS PubMed Google Scholar
• Wittbrodt, J., Shima, A. & Schartl, M. Medaka — a model organism from the Far East. Nature Rev. Genet. 3, 53–64 (2002).
  CAS PubMed Google Scholar