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Sequence comparison is a basic operation in DNA sequencing projects, and most of sequence comparison methods are based on heuristics, which are fast but not sensitive. The Dynamic Programming Algorithm, Smith-Waterman, obtains the best alignment, but at the expense of computational time. Unfortunately, the inefficiency in the performance of the Smith-Waterman algorithm limits its applications in the real world. A possible way out of this is to use parallelization methods for decreasing the time taken to execute the algorithm. In this paper, the authors present a two master method and a novel parallel technique called staircase method to improve the performance of the Smith-Waterman algorithm.
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