Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
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.
Bateman
A
A
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. agb@sanger.ac.uk
Birney
E
E
Durbin
R
R
Eddy
S R
SR
Finn
R D
RD
Sonnhammer
E L
EL
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
D011506:Proteins