ConFind: a robust tool for conserved sequence identification

被引：15

作者：

Smagala, JA ^{[1
]}

Dawson, ED ^{[1
]}

Mehlmann, M ^{[1
]}

Townsend, MB ^{[1
]}

Kuchta, RD ^{[1
]}

Rowlen, KL ^{[1
]}

机构：

[1] Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA

来源：

BIOINFORMATICS | 2005年 / 21卷 / 24期

关键词：

D O I：

10.1093/bioinformatics/bti719

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

ConFind (conserved region finder) identifies regions of conservation in multiple sequence alignments that can serve as diagnostic targets. Designed to work with a large number of closely related, highly variable sequences, ConFind provides robust handling of alignments containing partial sequences and ambiguous characters. Conserved regions are defined in terms of minimum region length, maximum informational entropy (variability) per position, number of exceptions allowed to the maximum entropy criterion and the minimum number of sequences that must contain a non-ambiguous character at a position to be considered for inclusion in a conserved region. Comparison of the calculated entropy for an alignment of 95 influenza A hemagglutinin sequences with random deletions results in a 98% reduction in the average error in ConFind relative to the 'Find Conserved Regions' option in BioEdit.

引用

页码：4420 / 4422

页数：3

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