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GPU accelerated Smith-Waterman

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (2006) 3994 LNCS - IV 188-195
DOI: 10.1007/11758549_29
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Abstract

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. © Springer-Verlag Berlin Heidelberg 2006.

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APA

Liu, Y., Huang, W., Johnson, J., & Vaidya, S. (2006). GPU accelerated Smith-Waterman. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 3994 LNCS-IV, pp. 188–195). Springer Verlag. https://doi.org/10.1007/11758549_29

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