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Optimal Alignment of Three Sequences On A GPU

We develop two algorithms–layered and sloped–to align three sequences on a GPU. Our algorithms can be used to determine the alignment score as well as the actual alignment. Experiments conducted using an NVIDIA C2050 GPU show that our sloped algorithm is 3 times as fast as the layered one. Further, the sloped algorithm delivers a speedup of up to 90 relative to the single core algorithm running on our host CPU when determining the score of the best alignment and a speedup between 21 and 56 when computing the best alignment as well as its score.