GPU Accelerated Smith-Waterman
- Cite this paper as:
- Liu Y., Huang W., Johnson J., Vaidya S. (2006) GPU Accelerated Smith-Waterman. In: Alexandrov V.N., van Albada G.D., Sloot P.M.A., Dongarra J. (eds) Computational Science – ICCS 2006. ICCS 2006. Lecture Notes in Computer Science, vol 3994. Springer, Berlin, Heidelberg
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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