The Pfam protein families database

被引：1508

作者：

Finn, Robert D. ^{[1
]}

Mistry, Jaina ^{[1
]}

Tate, John ^{[1
]}

Coggill, Penny ^{[1
]}

Heger, Andreas ^{[2
]}

Pollington, Joanne E. ^{[1
]}

Gavin, O. Luke ^{[1
]}

Gunasekaran, Prasad ^{[1
]}

Ceric, Goran ^{[3
]}

Forslund, Kristoffer ^{[4
]}

Holm, Liisa ^{[5
,6
]}

Sonnhammer, Erik L. L. ^{[4
]}

Eddy, Sean R. ^{[3
]}

Bateman, Alex ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Hinxton CB10 1SA, Cambs, England

[2] Univ Oxford, Dept Physiol Anat & Genet, MRC Funct Genom Unit, Oxford, England

[3] Howard Hughes Med Inst, Ashburn, VA 20147 USA

[4] Stockholm Univ, Stockholm Bioinformat Ctr, SE-10691 Stockholm, Sweden

[5] Univ Helsinki, Inst Biotechnol, Helsinki 00014, Finland

[6] Univ Helsinki, Dept Biol & Environm Sci, FIN-00014 Helsinki, Finland

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

基金：

芬兰科学院; 英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

TREES; BLAST;

D O I：

10.1093/nar/gkp985

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 similar to 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/).

引用

页码：D211 / D222

页数：12

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