NDLI: An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

Content Provider	IEEE Xplore Digital Library
Author	Bonny, T. Zidan, M.A. Salama, K.N.
Copyright Year	2010
Description	Author affiliation: Electrical Engineering Program, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia (Bonny, T.; Zidan, M.A.; Salama, K.N.)
Abstract	Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we introduce our Adaptive Hybrid Multiprocessor technique to accelerate the implementation of the Smith-Waterman algorithm. Our technique utilizes both the graphics processing unit (GPU) and the central processing unit (CPU). It adapts to the implementation according to the number of CPUs given as input by efficiently distributing the workload between the processing units. Using existing resources (GPU and CPU) in an efficient way is a novel approach. The peak performance achieved for the platforms GPU + CPU, GPU + 2CPUs, and GPU + 3CPUs is 10.4 GCUPS, 13.7 GCUPS, and 18.6 GCUPS, respectively (with the query length of 511 amino acid).
Starting Page	112
Ending Page	115
File Size	344859
Page Count	4
File Format	PDF
ISBN	9781424471683
ISSN	21566100
e-ISBN	9781424471706
DOI	10.1109/CIBEC.2010.5716098
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-12-16
Publisher Place	Egypt
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Databases Heuristic algorithms Amino acids Central Processing Unit Acceleration Bioinformatics Graphics processing unit
Content Type	Text
Resource Type	Article

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