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Reports (Research Report) Year : 2008

Fine-grained parallelization of similarity search between protein sequences

Abstract

This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore architectures or graphic boards. Three programs have been developed: PLAST-P, TPLAST-N and PLAST-X. They provide equivalent results compared to the NCBI BLAST family programs (BLAST-P, TBLAST-N and BLAST-X) with a speed-up factor ranging from 5 to 10.
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Dates and versions

inria-00275250 , version 1 (23-04-2008)
inria-00275250 , version 2 (23-04-2008)

Identifiers

  • HAL Id : inria-00275250 , version 1
  • ARXIV : 0804.3643

Cite

van Hoa Nguyen, Dominique Lavenier. Fine-grained parallelization of similarity search between protein sequences. [Research Report] 2008, pp.40. ⟨inria-00275250v1⟩
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