GPU accelerated smith-waterman

Authors:
Yang Liu;Wayne Huang;John Johnson;Sheila Vaidya
Affiliations:
Lawrence Livermore National Laboratory;Lawrence Livermore National Laboratory;Lawrence Livermore National Laboratory;Lawrence Livermore National Laboratory
Venue:
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part IV
Year:
2006

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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.