Ordered index seed algorithm for intensive DNA sequence comparison

@article{Lavenier2008OrderedIS,
  title={Ordered index seed algorithm for intensive DNA sequence comparison},
  author={Dominique Lavenier},
  journal={2008 IEEE International Symposium on Parallel and Distributed Processing},
  year={2008},
  pages={1-8}
}
  • D. Lavenier
  • Published 14 April 2008
  • Computer Science
  • 2008 IEEE International Symposium on Parallel and Distributed Processing
This paper presents a seed-based algorithm for intensive DNA sequence comparison. The novelty comes from the way seeds are used to efficiently generate small ungapped alignments - or HSPs (high scoring pairs) - in the first stage of the search. W-nt words are first indexed and all the Aw possible seeds are enumerated following a strict order ensuring fast generation of unique HSPs. A prototype - written in C - has been realized and tested on large DNA banks. Speed-up compared to BLASTN range… Expand

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