The Pfam protein families database

ROBERT FINN(Howard Hughes Medical Institute), Jaina Mistry(Howard Hughes Medical Institute), John Tate(Howard Hughes Medical Institute), Penny Coggill(Howard Hughes Medical Institute), Andreas Heger(Howard Hughes Medical Institute), Joanne E. Pollington(Howard Hughes Medical Institute), O. Luke Gavin(Howard Hughes Medical Institute), Prasad Gunasekaran(Howard Hughes Medical Institute), Goran Ceric(Howard Hughes Medical Institute), Kristoffer Forslund(Howard Hughes Medical Institute), Liisa Holm(University of Helsinki), Erik L. L. Sonnhammer(Howard Hughes Medical Institute), Sean R. Eddy(Howard Hughes Medical Institute), Alex Bateman(Howard Hughes Medical Institute)
Nucleic Acids Research
November 17, 2009
10.1093/nar/gkp985
Cited by 2,722Open Access
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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 approximately 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://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

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