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 model s of protein domain families. Release 3.1 is a major update of the Pfam dat abase 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.s e/Pfam/, and in the US at http://pfam.wustl.edu/. Over 54% of proteins in S WISS-PROT-35 and SP-TrEMBL-5 match a Pfam family, The primary changes of Pf am 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 fo r matches, and that it now includes proteins from both SP-TrEMBL-5 and SWIS S-PROT.