International Journal of Applied Science and Engineering
Published by Chaoyang University of Technology

Shyi-Ming Chen*, Chung-Hui Lin, and Shi-Jay Chen

Department of Computer Science and Information Engineering National Taiwan University of Science and Technology Taipei 106, Taiwan, R. O. C.


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Multiple DNA sequence alignment is one of the important research topics of bioinformatics. Because of the huge length of DNA sequences of advanced organisms, some researchers used divide-and-conquer techniques to cut the sequences for decreasing the space complexity for sequence alignment. Because the cutting points of sequences of the existing methods are fixed at the middle or the near-middle points, the performance of sequence alignment of the existing methods is not good enough. In this paper, we present a new method for multiple DNA sequence alignment using genetic algorithms and divide-and-conquer techniques to choose optimal cut points of multiple DNA sequences. The experimental results show that the proposed method is better than the existing method for dealing with multiple DNA sequence alignment.

Keywords: DNA sequences; sequence alignment; multiple sequence alignment; divide-and-conquer techniques; genetic algorithms.

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Accepted: 2005-05-04
Available Online: 2005-10-03

Cite this article:

Chen, S.-M., Lin, C.-H., Chen, S.-J., 2005. Multiple DNA sequence alignment based on genetic algorithms and Divide-and-Conquer techniques. International Journal of Applied Science and Engineering, 3, 89–100.

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