Software
PLAST: parallel local alignment search tool for database comparison
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Corresponding authors: Van Hoa Nguyen vhnguyen@irisa.fr - Dominique Lavenier lavenier@irisa.fr
1 Symbiose team-project, INRIA/IRISA, Campus de Beaulieu, 35042 Rennes Cedex, France
2 ENS Cachan Bretagne, Campus de Ker Lann, 35170 Bruz, France
BMC Bioinformatics 2009, 10:329 doi:10.1186/1471-2105-10-329
Published: 12 October 2009Abstract
Background
Sequence similarity searching is an important and challenging task in molecular biology and next-generation sequencing should further strengthen the need for faster algorithms to process such vast amounts of data. At the same time, the internal architecture of current microprocessors is tending towards more parallelism, leading to the use of chips with two, four and more cores integrated on the same die. The main purpose of this work was to design an effective algorithm to fit with the parallel capabilities of modern microprocessors.
Results
A parallel algorithm for comparing large genomic banks and targeting middle-range computers has been developed and implemented in PLAST software. The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set) and the multithreading concept (multicore). Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy.
Conclusion
A parallel algorithmic approach driven by the knowledge of the internal microprocessor architecture allows significant speedup to be obtained while preserving standard sensitivity for similarity search problems.