Computational Science – ICCS 2006

Volume 3994 of the series Lecture Notes in Computer Science pp 188-195

GPU Accelerated Smith-Waterman

  • Yang LiuAffiliated withLawrence Livermore National Laboratory
  • , Wayne HuangAffiliated withLawrence Livermore National LaboratoryDOE Joint Genome Institute, UCRL-CONF-218814
  • , John JohnsonAffiliated withLawrence Livermore National Laboratory
  • , Sheila VaidyaAffiliated withLawrence Livermore National Laboratory

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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.