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Fourth IEEE International Conference on Cluster Computing (CLUSTER'02)
Parallel Pattern Identification in Biological Sequences on Clusters
Chicago, Illinois
September 23-September 26
ISBN: 0-7695-1745-5
Chun-Hsi Huang, University of Connecticut
Ratnabali Biswas, University of Connecticut
This paper presents a low communication-overhead parallel algorithm for pattern matching in biological sequences. Given such a sequence of length n and a pattern of length m, we conclude an algorithm with five computation/communication phases, each requiring O(n) computation time and only O(p) message units. The low communication overhead of the algorithm is essential to achieving reasonable speedups on clusters, where the interprocessor communication latency is usually higher. Previous parallel implementations use straightforward domain decomposition based on existing sequential algorithms and rely on parallel machines with low-latency interconnection network and fast hardware support for processor synchronization.
Index Terms:
Parallel Algorithm, Pattern Matching, Cluster Computing
Citation:
Chun-Hsi Huang, Ratnabali Biswas, "Parallel Pattern Identification in Biological Sequences on Clusters," cluster, pp.127, Fourth IEEE International Conference on Cluster Computing (CLUSTER'02), 2002
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