title: Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
abstract: Pfam is a collection of multiple alignments and profile hidden Markov models of protein domain families. Release 3.1 is a major update of the Pfam database and contains 1313 families which are available on the World Wide Web in Europe at http://www.sanger.ac.uk/Software/Pfam/ and http://www.cgr.ki.se/Pfam/, and in the US at http://pfam.wustl.edu/. Over 54% of proteins in SWISS-PROT-35 and SP-TrEMBL-5 match a Pfam family. The primary changes of Pfam since release 2.1 are that we now use the more advanced version 2 of the HMMER software, which is more sensitive and provides expectation values for matches, and that it now includes proteins from both SP-TrEMBL and SWISS-PROT.
authors.affiliation: The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. agb@sanger.ac.uk
authors.forename: A
authors.initials: A
authors.lastname: Bateman
authors.forename: E
authors.initials: E
authors.lastname: Birney
authors.forename: R
authors.initials: R
authors.lastname: Durbin
authors.forename: S R
authors.initials: SR
authors.lastname: Eddy
authors.forename: R D
authors.initials: RD
authors.lastname: Finn
authors.forename: E L
authors.initials: EL
authors.lastname: Sonnhammer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D016208:Databases, Factual / Q000592:standards; D016247:Information Storage and Retrieval; D020407:Internet; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D011786:Quality Control; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software; D013223:Statistics as Topic
chemical_list: D011506:Proteins