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. 1998 Jan 1;26(1):320-2.
doi: 10.1093/nar/26.1.320.

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

E L Sonnhammer  1 , S R Eddy, E Birney, A Bateman, R Durbin
Affiliations

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

E L Sonnhammer et al. Nucleic Acids Res. .

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.

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References

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