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

被引:551
作者
Sonnhammer, ELL
Eddy, SR
Birney, E
Bateman, A
Durbin, R
机构
[1] Natl Lib Med, Natl Ctr Biotechnol Informat, Computat Biol Branch, Bethesda, MD 20894 USA
[2] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA
[3] Sanger Ctr, Cambridge CB10 1SA, England
基金
英国惠康基金;
关键词
D O I
10.1093/nar/26.1.320
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 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.
引用
收藏
页码:320 / 322
页数:3
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