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EM-Coffee: An Improvement of M-Coffee

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5 Author(s)
Nguyen Ha Anh Tuan ; Vietnam Nat. Univ., Univ. of Eng. & Technol., Hanoi, Vietnam ; Ha Tuan Cuong ; Nguyen Hoang Dung ; Le Sy Vinh
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Multiple sequence alignment is a basic of sequence analysis. In the development of multiple sequence alignment (MSA) approaches, M-Coffee [1] was proposed as a meta-method for assembling outputs from different individual multiple aligners into one single MSA to boost the accuracy. Authors showed that M-Coffee outperformed individual alignment methods. In this paper, we propose an improvement of M-coffee, called EM-Coffee, by introducing a new weighting scheme for combining input alignments. Experiments with benchmark datasets showed that EM-Coffee produced better results than M-Coffee, T-Coffee, Muscle and some other widely used methods. Thus, we provide an alternative option for researchers to align sequences.

Published in:

Knowledge and Systems Engineering (KSE), 2010 Second International Conference on

Date of Conference:

7-9 Oct. 2010