DocumentCode :
1093298
Title :
Streaming Algorithms for Biological Sequence Alignment on GPUs
Author :
Liu, Weiguo ; Schmidt, Bertil ; Voss, Gerrit ; Müller-Wittig, Wolfgang
Author_Institution :
Nanyang Technol. Univ., Singapore
Volume :
18
Issue :
9
fYear :
2007
Firstpage :
1270
Lastpage :
1281
Abstract :
Sequence alignment is a common and often repeated task in molecular biology. Typical alignment operations consist of finding similarities between a pair of sequences (pairwise sequence alignment) or a family of sequences (multiple sequence alignment). The need for speeding up this treatment comes from the rapid growth rate of biological sequence databases: every year their size increases by a factor of 1.5 to 2. In this paper, we present a new approach to high-performance biological sequence alignment based on commodity PC graphics hardware. Using modern graphics processing units (GPUs) for high-performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have reformulated dynamic-programming-based alignment algorithms as streaming algorithms in terms of computer graphics primitives. Our experimental results show that the GPU-based approach allows speedups of more than one order of magnitude with respect to optimized CPU implementations.
Keywords :
biology computing; computer graphics; dynamic programming; molecular biophysics; sequences; GPU; biological sequence alignment; biological sequence databases; commodity PC graphics hardware; dynamic-programming-based alignment algorithm; graphics processing units; molecular biology; multiple sequence alignment; pairwise sequence alignment; streaming algorithms; Acceleration; Biology computing; Central Processing Unit; Computer architecture; Computer graphics; Databases; Hardware; High performance computing; Runtime; Sequences; GPGPU; Streaming architectures; dynamic programming; graphics hardware; multiple sequence alignment; pairwise sequence alignment;
fLanguage :
English
Journal_Title :
Parallel and Distributed Systems, IEEE Transactions on
Publisher :
ieee
ISSN :
1045-9219
Type :
jour
DOI :
10.1109/TPDS.2007.1069
Filename :
4288126
Link To Document :
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