Protein domain identification and improved sequence similarity searching using PSI-BLAST

被引：48

作者：

George, RA ^{[1
]}

Heringa, J ^{[1
]}

机构：

[1] Natl Inst Med Res, Div Math Biol, London NW7 1AA, England

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2002年 / 48卷 / 04期

关键词：

domains; modules; PSI-BLAST; sequence; genome;

D O I：

10.1002/prot.10175

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：

Protein sequences containing more than one structural domain are problematic when used in homology searches where they can either stop an iterative database search prematurely or cause an explosion of a search to common domains. We describe a method, DOMAINATION, that infers domains and their boundaries in a query sequence from local gapped alignments generated using PSI-BLAST. Through a new technique to recognize domain insertions and permutations, DOMAINATION submits delineated domains as successive database queries in further iterative steps. Assessed over a set of 452 multidomain proteins, the method predicts structural domain boundaries with an overall accuracy of 50% and improves finding distant homologies by 14% compared with PSI-BLAST. DOMAINATION is available as a web based tool at http://mathbio.nimr.mrc.ac.uk, and the source code is available from the authors upon request. Proteins 2002;48:672-681. (C) 2002WiIey-Liss,lnc.

引用

页码：672 / 681

页数：10

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