CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
... Transactions on Parallel and Distributed Systems, vol. 99, PrePrints, 2012
[2] Edans Sandes, Alba Melo. Smith-Waterman Alignment of Huge Sequences with GPU in Linear Space. IPDPS 2011: 1199-1211
[3] Edans Sandes, Alba Melo. CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences. PPOPP 2010: 137-146
The latest source code can be found in Github. See the MASA project at https://github.com/edanssandes/MASA-CUDAlign