| Literature DB >> 24336227 |
Junjie Li1, Sanjay Ranka, Sartaj Sahni.
Abstract
We develop novel single-GPU parallelizations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative to competing GPU algorithms.Entities:
Keywords: CUDA; GPU; Long sequence alignment; Smith-Waterman algorithm; local alignment
Year: 2012 PMID： 24336227 PMCID： PMC3855353 DOI： 10.1109/ICCABS.2012.6182641
Source DB: PubMed Journal: IEEE Int Conf Comput Adv Bio Med Sci ISSN： 2164-229X