SW#-GPU-enabled exact alignments on genome scale.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 23864730.
- Also identified by DOI 10.1093/bioinformatics/btt410 and PMC identifier 3777108.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. Source code and installation instructions freely available for download at http://complex.zesoi.fer.hr/SW.html.
Medical subject headings
- Algorithms
- Genome