New powerful statistics for alignment-free sequence comparison under a pattern transfer model

被引：33

作者：

Liu, Xuemei ^{[1
,2
]}

Wan, Lin ^{[1
]}

Li, Jing ^{[1
]}

Reinert, Gesine ^{[3
]}

Waterman, Michael S. ^{[1
,4
]}

Sun, Fengzhu ^{[1
,4
]}

机构：

[1] Univ So Calif, Mol & Computat Biol Program, Los Angeles, CA 90089 USA

[2] S China Univ Technol, Sch Phys, Guangzhou, Guangdong, Peoples R China

[3] Univ Oxford, Dept Stat, Oxford OX1 3TG, England

[4] Tsinghua Univ, TNLIST Dept Automat, Beijing 100084, Peoples R China

来源：

JOURNAL OF THEORETICAL BIOLOGY | 2011年 / 284卷 / 01期

基金：

中国国家自然科学基金;

关键词：

Alignment-free sequence comparison; D-2; Pattern transfer model; K-WORD MATCHES; PHYLOGENETIC TREE RECONSTRUCTION; FEATURE FREQUENCY PROFILES; COMPOSITION VECTOR METHOD; WHOLE-PROTEOME PHYLOGENY; REGULATORY SEQUENCES; ASYMPTOTIC-BEHAVIOR; DNA; GENOMES; DISSIMILARITY;

D O I：

10.1016/j.jtbi.2011.06.020

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Alignment-free sequence comparison is widely used for comparing gene regulatory regions and for identifying horizontally transferred genes. Recent studies on the power of a widely used alignment-free comparison statistic D-2 and its variants D-2* and D-2(s) showed that their power approximates a limit smaller than 1 as the sequence length tends to infinity under a pattern transfer model. We develop new alignment-free statistics based on D-2, D-2* and D-2(s) by comparing local sequence pairs and then summing over all the local sequence pairs of certain length. We show that the new statistics are much more powerful than the corresponding statistics and the power tends to 1 as the sequence length tends to infinity under the pattern transfer model. (c) 2011 Elsevier Ltd. All rights reserved.

引用

页码：106 / 116

页数：11

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