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CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information:
[1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. IEEE 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
Categories
Bio-InformaticsLicense
GNU General Public License version 3.0 (GPLv3)Follow CUDAlign
User Reviews
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The MASA source code is now published in github
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The CUDAlign code could not be downloaded when I check, Oct 6, 2013. Clicks on the Git repository browser indicate that administrative rights are required. Recent literature confirms that this code is not publicly available. So, this project is impossible to review. On Sourceforge, where openness is important, I think this deserves one star.