http://www.comp.hkbu.edu.hk/~chxw/software/G-BLASTN.html
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 use the GPU and CPU resources when handling a batch of medium to large sized queries. Currently, G_BLASTN supports the blastn and megablast modes of NCBI-BLAST. The discontiguous megablast mode is not supported yet.
G-BLASTN is free software and you can browse/download the source code at sourceforge.net or github.
The current version of G-BLASTN is v1.1.