PFAM - MULTIPLE SEQUENCE ALIGNMENTS AND HMM-PROFILES OF PROTEIN DOMAINS

Pfam contains multiple alignments and hidden Markov model based profil es (HMM-profiles) of complete protein domains. The definition of domai n boundaries, family members and alignment is done semi-automatically based on expert knowledge, sequence similarity, other protein family d atabases and the ability of HMM-profiles to correctly identify and ali gn the members, Release 2.0 of Pfam contains 527 manually verified fam ilies which are available for browsing and on-line searching via the W orld Wide Web in the UK at http://www.sanger.ac.uk/Pfam/ and in the US at http://genome.wustl.edu/Pfam/Pfam 2.0 matches one or more domains in 50% of Swissprot-34 sequences, and 25% of a large sample of predict ed proteins from the Caenorhabditis elegans genome.