Title :
Pairwise sequence alignment for very long sequences on GPUs
Author :
Li, Junjie ; Ranka, Sanjay ; Sahni, Sartaj
Author_Institution :
Dept. of Comput. & Inf. Sci. & Eng., Univ. of Florida, Gainesville, FL, USA
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.
Keywords :
bioinformatics; graphics processing units; parallel architectures; Smith-Waterman algorithm; long sequence alignment; pairwise sequence alignment; single-GPU parallelization; Equations; Graphics processing unit; Heuristic algorithms; Kernel; Memory management; Parallel processing; Strips; CUDA; GPU; Long sequence alignment; Smith-Waterman algorithm; local alignment;
Conference_Titel :
Computational Advances in Bio and Medical Sciences (ICCABS), 2012 IEEE 2nd International Conference on
Conference_Location :
Las Vegas, NV
Print_ISBN :
978-1-4673-1320-9
Electronic_ISBN :
978-1-4673-1319-3
DOI :
10.1109/ICCABS.2012.6182641
