1887

Abstract

The explosion in the number of complete genomes over the past decade has spawned a new and exciting discipline, that of comparative genomics. To exploit the full potential of this approach requires the development of novel algorithms, databases and software which are sophisticated enough to draw meaningful comparisons between complete genome sequences and are widely accessible to the scientific community at large. This article reviews progress towards the development of computational tools and databases for organizing and extracting biological meaning from the comparison of large collections of genomes.

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2005-07-01
2024-04-19
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References

  1. Bernal A., Ear U., Kyrpides N. 2001; Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res 29:126–127 [CrossRef]
    [Google Scholar]
  2. Cole S. T., Eiglmeier K., Parkhill J. 41 other authors 2001; Massive gene decay in the leprosy bacillus. Nature 409:1007–1011 [CrossRef]
    [Google Scholar]
  3. Darling A. C., Mau B., Blattner F. R., Perna N. T. 2004; Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394–1403 [CrossRef]
    [Google Scholar]
  4. Feil E. J. 2004; Small change: keeping pace with microevolution. Nat Rev Microbiol 2:483–495 [CrossRef]
    [Google Scholar]
  5. Field D., Hughes J. 2005; Cataloguing our current genome collection. Microbiology 151:1016–1019 [CrossRef]
    [Google Scholar]
  6. Field D., Hughes J., Gray T. 2005; The GenomeMine database. http://www.genomics.ceh.ac.uk/GMINE/
    [Google Scholar]
  7. Guttman D. S., Dykhuizen D. E. 1994; Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266:1380–1383 [CrossRef]
    [Google Scholar]
  8. Haft D. H., Selengut J. D., Brinkac L. M., Zafar N., White O. 2005; Genome properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 21:293–306 [CrossRef]
    [Google Scholar]
  9. Hallin P. F., Ussery D. W. 2004; CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 20:3682–3686 [CrossRef]
    [Google Scholar]
  10. Hoebeke M., Nicolas P., Bessieres P. 2003; MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics 19:859–864 [CrossRef]
    [Google Scholar]
  11. Hohl M., Kurtz S., Ohlebusch E. 2002; Efficient multiple genome alignment. Bioinformatics 18 Suppl 1:S312–S320
    [Google Scholar]
  12. Holmes E. C., Worobey M., Rambaut A. 1999; Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol 16:405–409 [CrossRef]
    [Google Scholar]
  13. Kurtz S., Phillippy A., Delcher A. L., Smoot M., Shumway M., Antonescu C., Salzberg S. L. 2004; Versatile and open software for comparing large genomes. Genome Biol 5:R12 [CrossRef]
    [Google Scholar]
  14. Luikart G., England P. R., Tallmon D., Jordan S., Taberlet P. 2003; The power and promise of population genomics: from genotyping to genome typing. Nat Rev Genet 4:981–994
    [Google Scholar]
  15. Maiden M. C., Bygraves J. A., Feil E. 10 other authors 1998; Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–3145 [CrossRef]
    [Google Scholar]
  16. Miller W. 2001; Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics 17:391–397 [CrossRef]
    [Google Scholar]
  17. Oinn T., Addis M., Ferris J. 8 other authors 2004; Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20:3045–3054 [CrossRef]
    [Google Scholar]
  18. Peterson J. D., Umayam L. A., Dickinson T., Hickey E. K., White O. 2001; The comprehensive microbial resource. Nucleic Acids Res 29:123–125 [CrossRef]
    [Google Scholar]
  19. Ren Q., Kang K. H., Paulsen I. T. 2004; TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res 32:database issueD284–D288 [CrossRef]
    [Google Scholar]
  20. Roberts R. J., Karp P., Kasif S., Linn S., Buckley M. R. 2005 An Experimental Approach to Genome Annotation. Critical Issues Colloquia Report Washington, DC: American Society for Microbiology;
    [Google Scholar]
  21. Robinson D. A., Enright M. C. 2004; Evolution of Staphylococcus aureus by large chromosomal replacements. J Bacteriol 186:1060–1064 [CrossRef]
    [Google Scholar]
  22. Siew N., Azaria Y., Fischer D. 2004; The ORFanage: an ORFan database. Nucleic Acids Res 32:database issueD281–D283 [CrossRef]
    [Google Scholar]
  23. Smith J. M., Dowson C. G., Spratt B. G. 1991; Localized sex in bacteria. Nature 349:29–31 [CrossRef]
    [Google Scholar]
  24. Strimmer K., Pybus O. G. 2001; Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol 18:2298–2305 [CrossRef]
    [Google Scholar]
  25. Suhre K., Claverie J. M. 2004; FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res 32:database issueD273–D276 [CrossRef]
    [Google Scholar]
  26. Tatusov R. L., Fedorova N. D., Jackson J. D. 14 other authors 2003; The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41 [CrossRef]
    [Google Scholar]
  27. Tiwari B., Field D. 2005; A bioinformatics playground. LinuxUser and Developer 46:50–56
    [Google Scholar]
  28. Uchiyama I. 2003; MBGD: microbial genome database for comparative analysis. Nucleic Acids Res 31:58–62 [CrossRef]
    [Google Scholar]
  29. Welch R. A., Burland V. 16 other authors Plunkett G. 3rd 2002; Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli . Proc Natl Acad Sci U S A 99:17020–17024 [CrossRef]
    [Google Scholar]
  30. Wheeler D. L., Barrett T., Benson D. A. 26 other authors 2005; Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 33:database issueD39–D45
    [Google Scholar]
  31. Wilson G. A., Bertrand N., Patel Y., Hughes J. B., Feil E. J., Field D. 2005; Orphans as taxonomically restricted and ecologically important genes. Microbiology 151: in press
    [Google Scholar]
  32. Yang Z., Bielawski J. P. 2000; Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503 [CrossRef]
    [Google Scholar]
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