Fast scalable algorithm on LARPBS for sequence alignment

Authors:
Ling Chen;Chen Juan;Yi Pan
Affiliations:
Department of Computer Science, Yangzhou University, Yangzhou, P.R. China;Department of Computer Science, Yangzhou University, Yangzhou, P.R. China;Department of Computer Science, Georgia State University, Atlanta, GA
Venue:
ISPA'05 Proceedings of the 2005 international conference on Parallel and Distributed Processing and Applications
Year:
2005

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Abstract

Linear array with reconfigurable pipelined bus system (LARPBS) is a parallel computational model based on the optical bus system. In this paper, an O(1) time algorithm on LARPBS for prefix computation based on the maximum operation is presented. We also present a fast and efficient sequence alignment algorithm on LARPBS. For two sequences with length of m, n respectively, the algorithm can be implemented in O(mn/p) time with p processors(1≤p≤max{m,n}). Since the time complexity of the algorithm can be adjusted by choosing different number of processors p , the algorithm is highly scalable.