Optimal Alignment of Three Sequences On A GPU

Junjie Li, Sanjay Ranka, Sartaj Sahni
Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA
International Conference on Bioinformatics and Computational Biology (BICoB), 2014


   title={Optimal Alignment of Three Sequences On A GPU},

   author={Li, Junjie and Ranka, Sanjay and Sahni, Sartaj},



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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.
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