Smith-Waterman's New Clothes

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As bioinformatics software developers learn to better manipulate powerful desktop processors, the argument that hardware accelerators are the only serious option for speeding up search algorithms is no longer an open-and-shut case. That being said, some algorithms are more in need of a boost than others. Smith-Waterman, used for optimal local sequence alignments, has long been regarded as the precise yet time-consuming and processor-heavy workhorse of database search tools.

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