Pairwise Sequence Alignment for Very Long Sequences on GPUs

J. Li, S. Ranka, S. Sahni
Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611


   title={Multicore and GPU Algorithms for Nussinov RNA Folding},

   author={Sahni, Junjie Li Sanjay Ranka Sartaj}


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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.
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