GPU-BLAST: using graphics processors to accelerate protein sequence alignment

Motivation: 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. Results: Using a general-purpose graphics processing unit (GPU), we have developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST. 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. Availability: The source code of GPU-BLAST is freely available at http://archimedes.cheme.cmu.edu/biosoftware.html. Contact: sahinidis@cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online.