Relation between weight matrix and substitution matrix: motif search by similarity

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	Relation between weight matrix and substitution matrix: motif search by similarity
	Zheng, WM; Zheng, WM , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
刊名	BIOINFORMATICS
	2005
卷号	21 期号:7 页码:938-943
ISSN号	1367-4803
英文摘要	Motivation: The discovery of patterns shared by several sequences that differ greatly is a basic task in sequence analysis, and still a challenge. Several methods have been developed for detecting patterns. Methods commonly used for motif search include the Gibbs sampler, Expectation-Maximization (EM) algorithm and some intuitive greedy approaches. One cannot guarantee the optimality of the result produced by the Gibbs sampler in a single run. The deterministic EM methods tend to get trapped by local optima. Solutions found by greedy approaches are rarely sufficiently good. Results: A simple model describing a motif or a portion of local multiple sequence alignment is the weight matrix model, in which a motif is characterized with position-specific probabilities. Two substitution matrices are proposed to relate the sequence similarity with the weight matrix. Combining the substitution matrix and weight matrix, we examine three typical sets of protein sequences with increasing complexity. At a low score threshold for pair similarity, sliding windows are compared with a seed window to find the score sum, which provides a measure of statistical significance for multiple sequence comparison. Such a similarity analysis reveals many aspects of motifs. Blocks determined by similarity can be used to deduce a primary weight matrix or an improved substitution matrix. The algorithm successfully obtains the optimal solution for the test sets by just greedy iteration.
学科主题	Physics
URL标识	查看原文
WOS记录号	WOS:000227977800014
公开日期	2012-08-30
内容类型	期刊论文
源URL	[http://ir.itp.ac.cn/handle/311006/13846]
专题	理论物理研究所_理论物理所1978-2010年知识产出
通讯作者	Zheng, WM , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.
推荐引用方式 GB/T 7714	Zheng, WM,Zheng, WM , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China.. Relation between weight matrix and substitution matrix: motif search by similarity[J]. BIOINFORMATICS,2005,21(7):938-943.
APA	Zheng, WM,&Zheng, WM , Acad Sinica, Inst Theoret Phys, POB 2735, Beijing 100080, Peoples R China..(2005).Relation between weight matrix and substitution matrix: motif search by similarity.BIOINFORMATICS,21(7),938-943.
MLA	Zheng, WM,et al."Relation between weight matrix and substitution matrix: motif search by similarity".BIOINFORMATICS 21.7(2005):938-943.