The Basic Local Alignment Search Tool (BLAST) is the most widely used tool in bioinformatics, an area in which searching is becoming a highly time consuming task due to the ever increasing size of biological databases.  We have utilized Graphics Processing Units (GPUs) to accelerate BLAST by parallelizing the string matching algorithm [1].  The current version of GPU-BLAST performs protein alignment by using a workstation's multi-core CPU and a many-core GPU.  Compared to NCBI-BLAST, our implementation produces identical results and is 2�4 times faster.  GPU-BLAST is freely available at http://eudoxus.cheme.cmu.edu/gpublast/gpublast.html.  This presentation will provide an overview of GPU-BLAST, detail its design and architecture, and describe our current work on the topic, which expands the capabilities of GPU-BLAST to utilize multiple GPUs and perform DNA matching. [1]  Vouzis, P. and N. V. Sahinidis, GPU-BLAST: Using graphics processors to accelerate protein sequence alignment, Bioinformatics, 27, 182-188, 2011.

Biological sequence alignment with GPU-BLAST

246th National Meeting (2013)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.