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.

• Type: Journal
• Year: 1998
• Where: NAR
• Authors: Erik L. L. Sonnhammer, Sean R. Eddy, Ewan Birney, Alex Bateman, Richard Durbin
• Keywords: Multiple Alignments, NAR 1998, Pfam, Protein Family Databases