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G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of queries. G-BLASTN supports megablast and blastn mode. The discontiguous megablast mode is currently not supported.
Citation:
K. Zhao and X.-W. Chu, “G-BLASTN: Accelerating Nucleotide Alignment by Graphics Processors”, Oxford, Bioinformatics, 2014. http://bioinformatics.oxfordjournals.org/content/early/2014/01/24/bioinformatics.btu047.abstract?keytype=ref&ijkey=FkuzgmzzPTJss9c
G-BLASTN is free software and you can browse/download the source code at: https://sourceforge.net/p/gblastn or https://github.com/OpenHero/gblastn
Acknowledgement:
This project is supported by grant FRG2/11-12/158 from Hong Kong Baptist University. We also thank NVIDIA corporation for their donation of GPU cards.