Journal
BIOINFORMATICS
Volume 29, Issue 19, Pages 2494-2495Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btt410
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Funding
- Biomedical Research Council of A*STAR, Singapore
- Ministry of Education Science and Sports of Republic of Croatia [036-0362214-1987]
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We propose SW#, a new CUDA graphical processor unit-enabled and memory-efficient implementation of dynamic programming algorithm, for local alignment. It can be used as either a stand-alone application or a library. Although there are other graphical processor unit implementations of the Smith-Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm.
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