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Part of the book series: Methods and Tools in Biosciences and Medicine ((MTBM))

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Abstract

Until recently, molecular systematics was dominated by analyses of DNA sequences or derived peptide sequences generated by traditional cloning or PCR techniques. Many of these early studies were dependent upon only a single form of biological information, primary sequence. With the advent of genomic biology, multiple layers of biological information are available for comparative inquiry. It is possible to compare genomic DNA sequence and structure, mRNA sequence (via cDNAs), alternate transcript mRNAs, and peptide sequence with or without post-translation modifications. In the future it should also be possible to generate comparative, phylogenetically relevant data from 3-dimensional protein models, as well as from protein interaction assays, and possibly even microarrays. With the accelerating pace of data collection, it may be more time-consuming to assemble publicly available data than to generate one’s own complement of pertinent data.

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References

  1. Pennisi E (1999) Keeping genome data- 5 bases clean and up to date. Science 286: 447–450

    Article  PubMed  CAS  Google Scholar 

  2. Nature, 404, 916 (2000) News in Brief 6

    Google Scholar 

  3. Pruitt KD, Katz KS, Sicotte H, Maglott DR (2000) Introducing RefSeq and Locus-Link curated human genome resources at the NCBI. Trends Genet. 16(1): 44–47

    Article  PubMed  CAS  Google Scholar 

  4. Macauley J, Wang H, Goodman N (1998) 7 A model system for studying the integra-tion of molecular biology databases. Bioinformatics 14 (7): 575–82

    Article  PubMed  CAS  Google Scholar 

  5. Tatusov RL, Koonin EV, Lipman DJ, (1997) A genomic perspective on protein families. Science 278(5338): 631–7

    Article  PubMed  CAS  Google Scholar 

  6. Altschul SF, Madden TL, Schaffer AA, Zhang J et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402

    Article  PubMed  CAS  Google Scholar 

  7. Brenner SE, Chothia C and Hubbard TJ (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci USA 95: 6073–6078

    Article  PubMed  CAS  Google Scholar 

  8. Schultz J, Milpetz F, Bork P and Ponting CP (1998) SMART, a simple modular architecture research tool: Identification of signalling domains. Proc. Natl. Acad. Sci. USA 95: 5857–5864

    Article  PubMed  CAS  Google Scholar 

  9. Schultz J, Copley RR, Doerks T, Ponting CP et al. (2000) SMART: A Web-based tool for the study of genetically mobile domains. Nucleic Acids Res 28: 231–234

    Article  PubMed  CAS  Google Scholar 

  10. Curwen VA, Williams GW and Bard JBL (2000) GHOST: a gene homology online search tool. Trends in Genetics. 16(7): 321–323

    Article  PubMed  CAS  Google Scholar 

  11. Retief JD, Lynch KR and Pearson WR (1999) Panning for genes-a visual strategy for identifying novel gene orthologs and paralogs. Gen Res 9: 373–382

    CAS  Google Scholar 

  12. Muller GB and Wagner GP (1996) Homology, hox genes, and developmental integration. Amer. Zool. 36: 4–13

    Google Scholar 

  13. Ashburner M, Ball CA, Blake JA, Botstein D et al. (2000) Gene Ontology: tool for the unification of biology. Nat Genet. (1): 25–9

    Google Scholar 

  14. Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99–113

    Article  PubMed  CAS  Google Scholar 

  15. Reeck GR, de Haen C, Tller DC, Doolittle RF et al. (1987) “Homology” in proteins and nucleic acids: A terminology muddle and a way out of it. Cell 50: 667

    CAS  Google Scholar 

  16. Murray AW (2000) Whither Genomics? Genome Biology 1(1)003.1–003.6

    Article  Google Scholar 

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© 2002 Springer Basel AG

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Wray, C.G. (2002). Complex Model Organism Genome Databases. In: DeSalle, R., Giribet, G., Wheeler, W. (eds) Techniques in Molecular Systematics and Evolution. Methods and Tools in Biosciences and Medicine. Birkhäuser, Basel. https://doi.org/10.1007/978-3-0348-8125-8_7

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  • DOI: https://doi.org/10.1007/978-3-0348-8125-8_7

  • Publisher Name: Birkhäuser, Basel

  • Print ISBN: 978-3-7643-6257-7

  • Online ISBN: 978-3-0348-8125-8

  • eBook Packages: Springer Book Archive

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