Algorithms for loosely constrained multiple sequence alignment

Authors:
Bin Song;Feng-feng Zhou;Guo-liang Chen
Affiliations:
Department of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui, P. R. China;Department of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui, P. R. China;Department of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui, P. R. China
Venue:
CIS'04 Proceedings of the First international conference on Computational and Information Science
Year:
2004

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Abstract

For finding accurate and biologically meaningful multiple sequence alignment, it is required to consider a loosely constrained version of multiple sequence alignment. This paper is the first to define a loosely constrained multiple sequence alignment (LCMSA). And it also designs a complete algorithm for the loosely constrained pair-wise sequence alignment problem with the time complexity of O((α+1)n2(α+1)) and an approximation algorithm for LCMSA running in time O(k2(α+1)n2(α+1)), k and n is the number and the maximum length of input sequences, and α is the length of constrained sequence. In fact, α is small compared to n and it is reasonable to regard it as a constant. So, the former two algorithms run in polynomial time. Finally, a LCMSA software system is built up.