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GPU-BLAST specifications


Unique identifier OMICS_00995
Alternative name Graphics Processing Unit - Basic Local Alignment Search Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein queries
Output data Alignment of protein sequences
Operating system Unix/Linux
Programming languages C++
Parallelization CUDA
Computer skills Advanced
Version 2.2.28
Stability Stable
Maintained Yes




No version available



  • person_outline Nick Sahinidis <>

Publication for Graphics Processing Unit - Basic Local Alignment Search Tool

GPU-BLAST citations


Prefiltering Model for Homology Detection Algorithms on GPU

PMCID: 5170890
PMID: 28008220
DOI: 10.4137/EBO.S40877

[…] cost and performance. our research and proposed implementation has focused on parallelizing blast with gpu hardware. at this point, either liu et al. with cuda-blastp, vouzis and sahinidis with gpu-blast, or xiao et al. are based on the parallelization of all compute stages of ncbi blast. following this reasoning, liu et al. with cuda-blastp evaluated the performance of their proposed […]


GPU Acceleration of Sequence Homology Searches with Database Subsequence Clustering

PMCID: 4970815
PMID: 27482905
DOI: 10.1371/journal.pone.0157338

[…] [] with 4 cpu cores and 1.6-fold acceleration relative to the blastn mode of ncbi-blast with 4 cpu cores. on the other hand, gpu accelerated seed-and-extend algorithms for protein sequences, such as gpu-blast [] and cuda-blastp[], achieved limited success. gpu-blast [] and cuda-blastp[] with 1 gpu achieve 6-fold and 5- to 6-fold acceleration, respectively, relative to the blastp mode […]


Comparison of Acceleration Techniques for Selected Low Level Bioinformatics Operations

PMCID: 4748744
PMID: 26904094
DOI: 10.3389/fgene.2016.00005

[…] distributing the input data to multiple computers as well., additionally, adapted versions of blast running on special purpose hardware (fpga: timelogic ®tera-blast ™; timelogic division, ; gpu: gpu-blast; vouzis and sahinidis, , g-blastn; zhao and chu, ) exist., different use cases for sequencing genomic dna exist. an organism's genome can be sequenced for the first time, resulting in a de […]


Exploiting GPUs in Virtual Machine for BioCloud

PMCID: 3654629
PMID: 23710465
DOI: 10.1155/2013/939460

[…] to exploit gpus. manavski and valle suggested a gpu implementation of smith-waterman sequence alignment [], and vouzis and sahinidis transformed the blast tool to a gpu based application, named the gpu-blast []. the barracuda [] and the g-aligner [] are also kinds of short sequence alignment tool with gpu acceleration. , our approach for virtualizing and sharing of gpus is based on the gpu […]


Accelerating large scale protein structure alignments with graphics processing units

PMCID: 3309952
PMID: 22357132
DOI: 10.1186/1756-0500-5-116

[…] a gpu-based smith-waterman algorithm [] for pair-wise dna sequence alignment. later, the efficiency of sequence alignments has been continuously improved in [-]. vouzis and sahinidis developed gpu-blast (basic local alignment search tool) [] to accelerate ncbi-blast []. hung et al. developed a method for calculating rmsd (root mean square deviation) after superposition for ati gpu card []. […]

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GPU-BLAST institution(s)
Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA; Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA

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