The Pfam protein families database.
Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
Bateman
Alex
A
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. agb@sanger.ac.uk
Birney
Ewan
E
Cerruti
Lorenzo
L
Durbin
Richard
R
Etwiller
Laurence
L
Eddy
Sean R
SR
Griffiths-Jones
Sam
S
Howe
Kevin L
KL
Marshall
Mhairi
M
Sonnhammer
Erik L L
EL
D000818:Animals; D001665:Binding Sites; D003196:Computer Graphics; D030562:Databases, Protein; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D046911:Macromolecular Substances; D008390:Markov Chains; D010802:Phylogeny; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000502:physiology; D016415:Sequence Alignment
D046911:Macromolecular Substances; D011506:Proteins