GPU Accelerated Smith-Waterman

Yang Liu, Wayne Huang, John Johnson, Sheila Vaidya
Lawrence Livermore National Laboratory
In Computational Science – ICCS 2006 (2006), pp. 188-195.


   title={Gpu accelerated Smith-Waterman},

   author={Liu, Y. and Huang, W. and Johnson, J. and Vaidya, S.},

   journal={Computational Science–ICCS 2006},





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We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. The results demonstrate that our system’s performance is competitive with current optimized software packages.
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