NDLI: Streaming Algorithms for Biological Sequence Alignment on GPUs

Content Provider	IEEE Xplore Digital Library
Author	Liu Weiguo Schmidt, B. Voss, G. Muller-Wittig, W.
Copyright Year	1990
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.
Sponsorship	IEEE Computer Society
File Size	3956578
File Format	PDF
ISSN	10459219
Volume Number	18
Issue Number	9
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-09-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Sequences Computer graphics Computer architecture Databases Hardware Biology computing Central Processing Unit Runtime Acceleration High performance computing GPGPU Streaming architectures dynamic programming pairwise sequence alignment multiple sequence alignment graphics hardware
Content Type	Text
Resource Type	Article
Subject	Signal Processing Computational Theory and Mathematics Hardware and Architecture

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