A new repeat-masking method enables specific detection of homologous sequences

被引：113

作者：

Frith, Martin C. ^{[1
]}

机构：

[1] Computat Biol Res Ctr, Inst Adv Ind Sci & Technol, Sequence Anal Team, Koto Ku, Tokyo 1350064, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷 / 04期

关键词：

ACID SUBSTITUTION MATRICES; COMPARATIVE GENOMICS; DNA-SEQUENCES; DATABASE;

D O I：

10.1093/nar/gkq1212

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：

Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to strong similarities that are not homologies. Standard repeat-masking methods fail to eliminate this problem, and they are especially ill-suited to AT-rich DNA such as malaria and slime-mould genomes. We present a new repeat-masking method, tantan, which is motivated by the mechanisms that create simple repeats. This method thoroughly eliminates spurious homology predictions for DNA-DNA, protein-protein and DNA-protein comparisons. Moreover, it enables accurate homology search for non-coding DNA with extreme A + T composition.

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页数：8

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