The pfam protein families database

Alex Bateman; Ewan Birney; Lorenzo Cerruti; Richard Durbin; Laurence Etwiller; Sean R. Eddy; Sam Griffiths-Jones; Kevin L. Howe; Mhairi Marshall; Erik L L Sonnhammer

doi:10.1093/nar/30.1.276

The pfam protein families database

Alex Bateman, Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, Erik L L Sonnhammer

Research output: Contribution to journal › Article › peer-review

Abstract

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http:// pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.

Original language	English
Pages (from-to)	276-280
Number of pages	4
Journal	Nucleic acids research.
Volume	30
Issue number	1
DOIs	https://doi.org/10.1093/nar/30.1.276
Publication status	Published - 1 Jan 2002

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10.1093/nar/30.1.276Licence: CC BY

Cite this

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title = "The pfam protein families database",

abstract = "Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http:// pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.",

author = "Alex Bateman and Ewan Birney and Lorenzo Cerruti and Richard Durbin and Laurence Etwiller and Eddy, {Sean R.} and Sam Griffiths-Jones and Howe, {Kevin L.} and Mhairi Marshall and Sonnhammer, {Erik L L}",

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AU - Bateman, Alex

AU - Birney, Ewan

AU - Cerruti, Lorenzo

AU - Durbin, Richard

AU - Etwiller, Laurence

AU - Eddy, Sean R.

AU - Griffiths-Jones, Sam

AU - Howe, Kevin L.

AU - Marshall, Mhairi

AU - Sonnhammer, Erik L L

PY - 2002/1/1

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AB - Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http:// pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.

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EP - 280

JO - Nucleic acids research.

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The pfam protein families database

Abstract

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