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The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53,000 citations that this software has received in the past two decades, and the use of the word "blast" as a verb referring to biological sequence comparison. Any improvement in the execution speed of BLAST would be of great importance in the practice of bioinformatics, and facilitate coping with ever increasing sizes of biomolecular databases.
Using a general-purpose graphics processing unit (GPU), we have developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST (www.ncbi.nlm.nih.gov). In comparison to the sequential NCBI-BLAST, GPU-BLAST is nearly four times faster, while producing identical results.
Please cite the authors in any work or product based on this material:
Panagiotis D. Vouzis and Nikolaos V. Sahinidis, "GPU-BLAST: using graphics processors to accelerate protein sequence alignment," Vol. 27, no. 2, pages 182-188, Bioinformatics, 2011 (Open Access).
The GPU-BLAST paper was one of the top-ten highest downloaded articles published in Bioinformatics in 2011.