Genomes and the Protein Universe

  • Eugene V. Koonin
  • Michael Y. Galperin


We have now surveyed some of the principal methodological approaches of comparative genomics and the major evolutionary conclusions that can be inferred from genome comparisons. In this short chapter, we take a view of genomes from a different vantage point. We briefly describe the current understanding of the organization of the protein Universe and project it on genomes to reveal common and unique patterns.


Genome Evolution Adenylate Kinase Generalize Pareto Distribution Multidomain Protein Double Logarithmic Scale 
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Further reading

  1. 1.
    Barabasi AL. 2002. Linked: The New Science of Networks. Perseus Publishing, Cambridge, MA.Google Scholar
  2. 2.
    Coulson AF, Moult J. 2002. A unifold, mesofold, and superfold model of protein fold use. Proteins 46, 61–71.PubMedCrossRefGoogle Scholar
  3. 3.
    Huynen MA, van Nimwegen E. 1998. The frequency distribution of gene family sizes in complete genomes. Molecular Biology and Evolution 15, 583–589.PubMedCrossRefGoogle Scholar
  4. 4.
    Koonin EV, Aravind L, Kondrashov AS. 2000. The impact of comparative genomics on our understanding of evolution. Cell 101, 573–576.PubMedCrossRefGoogle Scholar
  5. 5.
    Qian J, Luscombe NM, Gerstein M. 2001. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. Journal of Molecular Biology 313, 673–681.PubMedCrossRefGoogle Scholar
  6. 6.
    Vitkup D, Melamud E, Moult J, Sander C. 2001. Completeness in structural genomics. Nature Structural Biology 8, 559–566.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2003

Authors and Affiliations

  • Eugene V. Koonin
    • 1
  • Michael Y. Galperin
    • 1
  1. 1.National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthUSA

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