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BRENDA, the enzyme database: updates and major new developments

Nucleic Acids Research
Oxford University Press
Publication Date
DOI: 10.1093/nar/gkh081
  • Articles
  • Biology
  • Computer Science


gkp985 211..222 The Pfam protein families database Robert D. Finn1,*, Jaina Mistry1, John Tate1, Penny Coggill1, Andreas Heger2, Joanne E. Pollington1, O. Luke Gavin1, Prasad Gunasekaran1, Goran Ceric3, Kristoffer Forslund4, Liisa Holm5, Erik L. L. Sonnhammer4, Sean R. Eddy3 and Alex Bateman1 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, 2Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, UK, 3Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA, 4Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden and 5Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 (Viikinkaari 5), 00014 Helsinki, Finland Received October 12, 2009; Accepted October 15, 2009 ABSTRACT Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is �100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11 912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://, the USA (http://pfam.janelia .org/) and Sweden ( INTRODUCTION Pfam is a comprehensive database of conserved protein families. This collection of nearly 12 000 families is used extensively throughout the biological sciences, by experi- mental biologists researching specific proteins, computational biologists who need to organise sequences, and evoluti

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