SW#–GPU-enabled exact alignments on genome scale
Authors:
Open Access
- 31 July 2013
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 29 (19) , 2494-2495
Abstract
Summary: 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. Availability: Source code and installation instructions freely available for download at http://complex.zesoi.fer.hr/SW.html. Contact: mile.sikic@fer.hr Supplementary information: Supplementary Data are available at Bioinformatics online.Keywords
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