title: The Pfam protein families database.
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/).
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. rdf@sanger.ac.uk
authors.forename: Robert D
authors.initials: RD
authors.lastname: Finn
authors.forename: Jaina
authors.initials: J
authors.lastname: Mistry
authors.forename: John
authors.initials: J
authors.lastname: Tate
authors.forename: Penny
authors.initials: P
authors.lastname: Coggill
authors.forename: Andreas
authors.initials: A
authors.lastname: Heger
authors.forename: Joanne E
authors.initials: JE
authors.lastname: Pollington
authors.forename: O Luke
authors.initials: OL
authors.lastname: Gavin
authors.forename: Prasad
authors.initials: P
authors.lastname: Gunasekaran
authors.forename: Goran
authors.initials: G
authors.lastname: Ceric
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Forslund
authors.forename: Liisa
authors.initials: L
authors.lastname: Holm
authors.forename: Erik L L
authors.initials: EL
authors.lastname: Sonnhammer
authors.forename: Sean R
authors.initials: SR
authors.lastname: Eddy
authors.forename: Alex
authors.initials: A
authors.lastname: Bateman
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020745:Genome, Archaeal; D016681:Genome, Fungal; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software