title: Pfam: multiple sequence alignments and HMM-profiles of protein domains.
abstract: 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.
authors.affiliation: 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
authors.forename: E L
authors.initials: EL
authors.lastname: Sonnhammer
authors.forename: S R
authors.initials: SR
authors.lastname: Eddy
authors.forename: E
authors.initials: E
authors.lastname: Birney
authors.forename: A
authors.initials: A
authors.lastname: Bateman
authors.forename: R
authors.initials: R
authors.lastname: Durbin
mesh_terms: 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
chemical_list: D011506:Proteins