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Briefings in Bioinformatics Advance Access originally published online on March 15, 2008
Briefings in Bioinformatics 2008 9(3):210-219; doi:10.1093/bib/bbn010
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Pfam 10 years on: 10 000 families and still growing

Stephen John Sammut, Robert D. Finn and Alex Bateman

Corresponding author. Alex Bateman, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK. Tel: 44-1223-494950; Fax: 44-1223-494919; E-mail: agb{at}sanger.ac.uk

Classifications of proteins into groups of related sequences are in some respects like a periodic table for biology, allowing us to understand the underlying molecular biology of any organism. Pfam is a large collection of protein domains and families. Its scientific goal is to provide a complete and accurate classification of protein families and domains. The next release of the database will contain over 10 000 entries, which leads us to reflect on how far we are from completing this work. Currently Pfam matches 72% of known protein sequences, but for proteins with known structure Pfam matches 95%, which we believe represents the likely upper bound. Based on our analysis a further 28 000 families would be required to achieve this level of coverage for the current sequence database. We also show that as more sequences are added to the sequence databases the fraction of sequences that Pfam matches is reduced, suggesting that continued addition of new families is essential to maintain its relevance.

Keywords: Pfam, protein families, classification, coverage, hidden Markov model

Submitted: October 15, 2007. Received (in revised form): February 6, 2008.


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