MANGO: a new approach to multiple sequence alignment.

MANGO: a new approach to multiple sequence alignment. Research Abstract Details 

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MANGO: a new approach to multiple sequence alignment. Abstract Text:

Zefeng Zhang,Hao Lin,Ming Li,Zefeng Zhang,Hao Lin,Ming Li,

Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.

MANGO: a new approach to multiple sequence alignment. Publishing Authors By Initials

Z Zhang,H Lin,M Li,Z Zhang,H Lin,M Li,

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MANGO: a new approach to multiple sequence alignment. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Computational systems bioinformatics / Life Scienc

VOLUME: 6

Page Numbers: 237-47

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ISSN: 1752-7791

DAY: 22

MONTH: 10

YEAR: 2007

MANGO: a new approach to multiple sequence alignment. Information

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LANGUAGE: eng

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AFFILIATION: Computational Biology Research Group, Division of Intelligent Software Systems, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China. zhangzf@ict.ac.cn

Country: United States

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MEDLINETA: Comput Syst Bioinformatics Con

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