MSAID: multiple sequence alignment based on a measure of information discrepancy

doi:10.1016/j.compbiolchem.2004.12.005

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	MSAID: multiple sequence alignment based on a measure of information discrepancy
	Zhang, M ; Fang, WW ; Zhang, JH; Chi, ZX
	2005-04-01
发表期刊	COMPUTATIONAL BIOLOGY AND CHEMISTRY
ISSN	1476-9271
卷号	29 期号:2 页码:175-181
摘要	We propose an algorithm of global multiple sequence alignment that is based on a measure of what we call information discrepancy. The algorithm follows a progressive alignment iteration strategy that makes use of what we call a function of degree of disagreement (FDOD). MSAID begins with distance calculation of pairwise sequences, based on FDOD as a numerical scoring measure. In the next step, the resulting distance matrix is used to construct a guide tree via the neighbor-joining method. The tree is then used to produce a multiple alignment. Current alignment is next used to produce a new matrix and a new tree (with FDOD scoring measure again). This iterative process continues until convergence criteria (or a stopping rule) are satisfied. MSAID was tested and compared with other prior methods by using reference alignments from BAliBASE 2.01. For the alignments with no large N/C-terminal extensions or internal insertions MSAID received the top overall average in the tests. Moreover, the results of testing indicate that MSAID performs as well as other alignment methods with an occasional tendency to perform better than these prior techniques. We, therefore, believe that MSAID is a solid and reliable method of choice, which is often (if not always) superior to other global alignment techniques. (c) 2004 Published by Elsevier Ltd.
关键词	multiple sequence alignment progressive alignment iterative strategy FDOD measure
DOI	10.1016/j.compbiolchem.2004.12.005
语种	英语
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Computer Science
WOS类目	Biology ; Computer Science, Interdisciplinary Applications
WOS记录号	WOS:000228764000011
出版者	ELSEVIER SCI LTD
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/1177
专题	应用数学研究所
通讯作者	Zhang, M
作者单位	1.Dalian Univ Technol, Dept Comp Sci & Engn, Dalian 116024, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 3.Dalian Univ, Coll Informat Engn, Dalian 116622, Peoples R China
推荐引用方式 GB/T 7714	Zhang, M,Fang, WW,Zhang, JH,et al. MSAID: multiple sequence alignment based on a measure of information discrepancy[J]. COMPUTATIONAL BIOLOGY AND CHEMISTRY,2005,29(2):175-181.
APA	Zhang, M,Fang, WW,Zhang, JH,&Chi, ZX.(2005).MSAID: multiple sequence alignment based on a measure of information discrepancy.COMPUTATIONAL BIOLOGY AND CHEMISTRY,29(2),175-181.
MLA	Zhang, M,et al."MSAID: multiple sequence alignment based on a measure of information discrepancy".COMPUTATIONAL BIOLOGY AND CHEMISTRY 29.2(2005):175-181.