GPU Accelerated Smith-Waterman

  • Yang Liu
  • Wayne Huang
  • John Johnson
  • Sheila Vaidya
Conference paper

DOI: 10.1007/11758549_29

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3994)
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

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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Yang Liu
    • 1
  • Wayne Huang
    • 1
    • 2
  • John Johnson
    • 1
  • Sheila Vaidya
    • 1
  1. 1.Lawrence Livermore National Laboratory 
  2. 2.DOE Joint Genome Institute, UCRL-CONF-218814 

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