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PMID: 19920124 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The Pfam protein families database.

Nucleic acids research ·Vol. 38 ·No. Database issue ·2010-01-00 ·Pages D211-22

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A

Abstract

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

MeSH Terms

Amino Acid Sequence Animals Computational Biology/methods,trends Databases, Nucleic Acid Databases, Protein Genome, Archaeal Genome, Fungal Humans Information Storage and Retrieval/methods Internet Molecular Sequence Data Protein Structure, Tertiary Sequence Alignment Sequence Homology, Amino Acid Software

Authors & Affiliations

14 authors, click to expand affiliations / ORCID

Finn Robert D

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. rdf@sanger.ac.uk

Mistry Jaina

Tate John

Coggill Penny

Heger Andreas

Pollington Joanne E

Gavin O Luke

Gunasekaran Prasad

Ceric Goran

Forslund Kristoffer

Holm Liisa

Sonnhammer Erik L L

Eddy Sean R

Bateman Alex

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Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gkp985

rdf@sanger.ac.uk

Published

2010-01-00

Epub

2009-00-17

Pages

D211-22

Language

English

Region

England

NLM ID

0411011

PMCID

PMC2808889

Subset

Grants

Medical Research Council · MC_U137761446 · United Kingdom

Howard Hughes Medical Institute · United States

Wellcome Trust · 087656 · United Kingdom

Wellcome Trust · WT077044/Z/05/Z · United Kingdom

Biotechnology and Biological Sciences Research Council · BB/F010435/1 · United Kingdom

External Links

PubMed source DOI: 10.1093/nar/gkp985 PMC Full Text View journal details

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