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We develop novel single-GPU parallelizations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative to competing GPU algorithms.doi:10.1504/ijbra.2014.062989 pmid:24989857 fatcat:xqsopaoedjcd3gsdzufrqycvz4