Sequence motif databases Pfam Pfam is a database of protein families defined as domains (contiguous segments of entire protein sequences). For each domain, it contains a multiple alignment of a set of defining sequences (the seeds) and the other sequences in SWISS-PROT and TrEMBL that can be matched to that alignment. The database was started in 1996 and is maintained by a consortium of scientists, among them Erik Sonnhammer (CGB, KI, Sweden), Sean Eddy (WashU, St Louis USA), Richard Durbin, Alan Bateman and Ewan Birney (Sanger Centre, UK). Release 6.6 (Sep 2001) contains 3,071 families. The alignments can be converted into hidden Markov models (HMM), which can be used to search for domains in a query protein sequence. The software HMMER (by Sean Eddy) is the computational foundation for Pfam. The domain structure of protein sequences in SWISS-PROT and TrEMBL are available directly from the Pfam web sites, and it is also possible to search for domains in other sequences using servers at
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