A Parallel Smith-Waterman Algorithm Based on Divide and Conquer

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ICA3PP '02 Proceedings of the Fifth International Conference on Algorithms and Architectures for Parallel Processing
Year:
2002

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Abstract

Biological sequence comparison is an important toolfor researchers in molecular biology. There are severalalgorithms for sequence comparison. TheSmith-Waterman algorithm, based on dynamicprogramming, is one of the most fundamental algorithmsin bioinformatics. However the existing parallelSmith-Waterman algorithm needs large memory space.As the data of biological sequences expand rapidly, thememory requirement of the existing parallelSmith-Waterman algorithm has becoming a criticalproblem. For resolving this problem, we develop a newparallel Smith-Waterman algorithm using the method ofdivide and conquer, named PSW-DC. Memory spacerequired in the new parallel algorithm is reducedsignificantly in comparison with existing ones. A keytechnique, named The C&E method, is developed for theimplementation of the new parallel Smith-Watermanalgorithm.