CUDAlign
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CUDAlign is a software that is able to align DNA sequences of unrestricted size with the Smith-Waterman algorithm combined with Myers-Miller. It uses the NVIDIA CUDA platform for accelerating the computation time. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. For chromosomes with 33 and 47 million base pairs, CUDAlign can produce the optimal alignment in less than 9 hours. 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
CUDAlign License - GNU General Public License version 3.0 (GPLv3)
Free download from Shareware Connection - CUDAlign is a software that is able to align DNA sequences of unrestricted size with the Smith-Waterman algorithm combined with Myers-Miller.
Version: 1.0 | Platform: WinOther
Released Date: | Rating: 0 | Title: CUDAlign
Author Url: http://sourceforge.net/projects/cudalign
Program Info Url: http://sourceforge.net/projects/cudalign
Download Url: http://sourceforge.net/projects/cudalign
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