GPU Accelerated Smith-Waterman
GPU Accelerated Smith-Waterman
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.
- Lawrence Berkeley National Laboratory United States
- Joint Genome Institute United States
- Lawrence Livermore National Laboratory United States
- University of North Texas United States
59 Basic Biological Sciences, Dynamic Programming, Implementation, Parallel Processing, Performance, And Information Science, Computing, Proteins, Dna, Processing, 99 General And Miscellaneous//Mathematics
59 Basic Biological Sciences, Dynamic Programming, Implementation, Parallel Processing, Performance, And Information Science, Computing, Proteins, Dna, Processing, 99 General And Miscellaneous//Mathematics
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