Fine-grained parallelization of similarity search between protein sequences

Details Fine-grained parallelization of similarity search between protein sequences Fine-grained parallelization of similarity search between protein sequences

2008-04-23

arxiv.org/abs/0804.3643v1

Biology

Quantitative Biology

Quantitative Methods

Scientific paper

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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