Fast sequence similarity computing with LCS on LARPBS

Authors:
Xiaohua Xu;Ling Chen;Ping He
Affiliations:
Department of Computer Science and Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China;Department of Computer Science, Yangzhou University, Yangzhou, China;Department of Computer Science, Yangzhou University, Yangzhou, China
Venue:
ISPA'05 Proceedings of the 2005 international conference on Parallel and Distributed Processing and Applications
Year:
2005

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Abstract

The problem of the longest common subsequence (LCS) is a fundamental problem in sequence alignment. In this paper, we first present fast parallel algorithms for sequence similarity with LCS. For two sequences of lengths m and n (m ≤ n), the algorithm uses n processors and costs O(m) computation time. Time-area cost of the algorithm is O(mn) which reaches optimality. Based on this algorithm, we also give a fast parallel algorithm which can compute the length of LCS in O(logm) time. To our best knowledge, this is the fastest one among the parallel LCS algorithms on array architectures.