Title: Pairwise sequence alignment for very long sequences on GPUs

Authors: Junjie Li; Sanjay Ranka; Sartaj Sahni

Addresses: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL-32611, USA ' Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL-32611, USA ' Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL-32611, USA

Abstract: 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.

Keywords: pairwise sequence alignment; local alignment; Smith-Waterman algorithm; CUDA; GPU; graphics processing units; bioinformatics.

DOI: 10.1504/IJBRA.2014.062989

International Journal of Bioinformatics Research and Applications, 2014 Vol.10 No.4/5, pp.345 - 368

Published online: 24 Oct 2014 *

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