Fine-grained parallelization of similarity search between protein sequences

TL;DR

This paper introduces parallelized algorithms for protein sequence comparison that significantly accelerate the process while maintaining comparable accuracy to existing BLAST tools.

Contribution

It presents three new programs optimized for parallel hardware, achieving 5 to 10 times faster performance than traditional BLAST programs.

Findings

Speed-up factor of 5 to 10 times over BLAST

Equivalent results to NCBI BLAST programs

Effective utilization of parallel hardware architectures

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.