Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

  title={Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation},
  author={Torbj\orn Rognes},
  booktitle={BMC Bioinformatics},
The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different… CONTINUE READING
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