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Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System
Joint Authors
Hung, Che-Lun
Liu, Yu
Hong, Yang
Lin, Chun-Yuan
Source
International Journal of Genomics
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-10-19
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics.
Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations.
However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one.
Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system.
Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments.
The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.
American Psychological Association (APA)
Liu, Yu& Hong, Yang& Lin, Chun-Yuan& Hung, Che-Lun. 2015. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System. International Journal of Genomics،Vol. 2015, no. 2015, pp.1-12.
https://search.emarefa.net/detail/BIM-1066043
Modern Language Association (MLA)
Liu, Yu…[et al.]. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System. International Journal of Genomics No. 2015 (2015), pp.1-12.
https://search.emarefa.net/detail/BIM-1066043
American Medical Association (AMA)
Liu, Yu& Hong, Yang& Lin, Chun-Yuan& Hung, Che-Lun. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System. International Journal of Genomics. 2015. Vol. 2015, no. 2015, pp.1-12.
https://search.emarefa.net/detail/BIM-1066043
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1066043