The Pfam protein families database.
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/).
Finn
Robert D
RD
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. rdf@sanger.ac.uk
Mistry
Jaina
J
Tate
John
J
Coggill
Penny
P
Heger
Andreas
A
Pollington
Joanne E
JE
Gavin
O Luke
OL
Gunasekaran
Prasad
P
Ceric
Goran
G
Forslund
Kristoffer
K
Holm
Liisa
L
Sonnhammer
Erik L L
EL
Eddy
Sean R
SR
Bateman
Alex
A
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