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This article is part of the supplement: Symposium of Computations in Bioinformatics and Bioscience (SCBB06)

Open Access Research

A fast parallel algorithm for finding the longest common sequence of multiple biosequences

Yixin Chen1*, Andrew Wan1 and Wei Liu2

Author Affiliations

1 Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA

2 Department of Computer Science, Yangzhou University, Yangzhou 225009, China

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BMC Bioinformatics 2006, 7(Suppl 4):S4  doi:10.1186/1471-2105-7-S4-S4

Published: 12 December 2006

Abstract

Background

Searching for the longest common sequence (LCS) of multiple biosequences is one of the most fundamental tasks in bioinformatics. In this paper, we present a parallel algorithm named FAST_LCS to speedup the computation for finding LCS.

Results

A fast parallel algorithm for LCS is presented. The algorithm first constructs a novel successor table to obtain all the identical pairs and their levels. It then obtains the LCS by tracing back from the identical character pairs at the last level. Effective pruning techniques are developed to significantly reduce the computational complexity. Experimental results on gene sequences in the tigr database show that our algorithm is optimal and much more efficient than other leading LCS algorithms.

Conclusion

We have developed one of the fastest parallel LCS algorithms on an MPP parallel computing model. For two sequences X and Y with lengths n and m, respectively, the memory required is max{4*(n+1)+4*(m+1), L}, where L is the number of identical character pairs. The time complexity is O(L) for sequential execution, and O(|LCS(X, Y)|) for parallel execution, where |LCS(X, Y)| is the length of the LCS of X and Y. For n sequences X1, X2, ..., Xn, the time complexity is O(L) for sequential execution, and O(|LCS(X1, X2, ..., Xn)|) for parallel execution. Experimental results support our analysis by showing significant improvement of the proposed method over other leading LCS algorithms.