DocumentCode
1809050
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
fYear
2012
fDate
23-25 Feb. 2012
Firstpage
1
Lastpage
6
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;
fLanguage
English
Publisher
ieee
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
Type
conf
DOI
10.1109/ICCABS.2012.6182641
Filename
6182641
Link To Document