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 110,000 citations that this software has received in the past three 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 ( 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.

The GPU-BLAST source code (C++ and CUDA) is freely available

GPU-BLAST supports:

  • protein alignment according to "blastp" (it does not support "psiblast")
  • multiple CPU threads working in parallel with a single GPU
  • input files with multiple protein queries

The code has been tested on Fedora 10, CentOS 5.5 and CentOS 6.6 with NVIDIA Tesla C1060 and C2050 GPUs, and with CUDA 2.3, 3.1, 3.2, 5.0.

External links (we neither endorse nor guarantee the quality of these links but offer them as they may be useful to users of GPU-BLAST):