GPU-BLAST is an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). The implementation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interface while producing identical results. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.
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Panagiotis D. Vouzis and Nikolaos V. Sahinidis,
“GPU-BLAST: using graphics processors to accelerate protein sequence alignment,”
Bioinformatics, 2011 Vol. 27, no. 2, pages 182-188,