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Nucleic Acids Research, 2003, Vol. 31, No. 15 4632-4638
© 2003 Oxford University Press

Protein families and TRIBES in genome sequence space

Anton J. Enright, Victor Kunin and Christos A. Ouzounis*

Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK

*To whom correspondence should be addressed. Tel: +44 1223 494653; Fax: +44 1223 494471; Email: ouzounis{at}ebi.ac.uk
Present address:
Anton J. Enright, Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box no. 460, New York, NY 10021, USA
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Accurate detection of protein families allows assignment of protein function and the analysis of functional diversity in complete genomes. Recently, we presented a novel algorithm called TribeMCL for the detection of protein families that is both accurate and efficient. This method allows family analysis to be carried out on a very large scale. Using TribeMCL, we have generated a resource called TRIBES that contains protein family information, comprising annotations, protein sequence alignments and phylogenetic distributions describing 311 257 proteins from 83 completely sequenced genomes. The analysis of at least 60 934 detected protein families reveals that, with the essential families excluded, paralogy levels are similar between prokaryotes, irrespective of genome size. The number of essential families is estimated to be between 366 and 426. We also show that the currently known space of protein families is scale free and discuss the implications of this distribution. In addition, we show that smaller families are often formed by shorter proteins and discuss the reasons for this intriguing pattern. Finally, we analyse the functional diversity of protein families in entire genome sequences. The TRIBES protein family resource is accessible at http://www.ebi.ac.uk/research/cgg/tribes/.


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