title: Pairwise Sequence Alignment for Very Long Sequences on GPUs.
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.
authors: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611.
authors: Junjie
authors: J
authors: Li
authors: Sanjay
authors: S
authors: Ranka
authors: Sartaj
authors: S
authors: Sahni
keywords: CUDA; GPU; Long sequence alignment; Smith-Waterman algorithm; local alignment