Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Pfam contains multiple alignments and hidden Markov model based profiles (HMM-profiles) of complete protein domains. The definition of domain boundaries, family members and alignment is done semi-automatically based on expert knowledge, sequence similarity, other protein family databases and the ability of HMM-profiles to correctly identify and align the members. Release 2.0 of Pfam contains 527 manually verified families which are available for browsing and on-line searching via the World 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 predicted proteins from the Caenorhabditis elegans genome.
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Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Building 38A, Room 8N805, National Institutes of Health, Bethesda, MD 20894, USA. sonnhammer@ncbi.nlm.nih.gov
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D000595:Amino Acid Sequence; D000818:Animals; D017173:Caenorhabditis elegans; D003195:Computer Communication Networks; D016208:Databases, Factual; D016247:Information Storage and Retrieval; D008390:Markov Chains; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
D011506:Proteins