Pairwise sequence alignment for very long sequences on GPUs
Junjie Li, Sanjay Ranka, Sartaj K. Sahni · International Journal of Bioinformatics Research and Applications · 2014
We develop novel single-GPU parallelisations 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.