The Pfam protein families database.
The Pfam protein families database.
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DOI：
10.1093/nar/gkp985
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发表时间：
2010-01
影响因子：
14.9
通讯作者：
Bateman A
中科院分区：
文献类型：
--
作者：
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
Pfam是一个广泛使用的蛋白质家族和结构域数据库。本文介绍了我们在最新版本（版本24.0）中实现的一组主要更新。最重要的变化是，我们现在使用HMMER 3，流行的配置文件隐马尔可夫模型包的最新版本。该软件比HMMER 2快100倍，并且由于常规使用前向算法而更敏感。迁移到HMMER 3需要对Pfam进行许多更改，详细描述了这些更改。PFAM第24.0版包含11912个系列，其中大量系列在过去两年中进行了重大更新。可通过联合王国（http：//pfam.sanger.ac.uk/）、美国（http：//pfam.janelia.org/）和瑞典（http：//pfam.sbc.su.se/）的服务器查阅该网站。
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 ∼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/).