Work

Pfam: multiple sequence alignments and HMM-profiles of protein domains

Year: 1998

Type: article

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.

Source: Nucleic Acids Research

DOI: 10.1093/nar/26.1.320

Authors: E. Sonnhammer, S R Eddy, E Birney, A Bateman, R Durbin

Institutions: National Institutes of Health, National Center for Biotechnology Information

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: Wellcome Trust, National Institutes of Health, National Human Genome Research Institute

Award: Probabilistic models of protein and RNA structure