Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
Joint Authors
Huang, Liang-Tsung
Wu, Chao-Chin
Lai, Lien-Fu
Li, Yun-Ju
Source
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-08-03
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Sequence alignment lies at heart of the bioinformatics.
The Smith-Waterman algorithm is one of the key sequence search algorithms and has gained popularity due to improved implementations and rapidly increasing compute power.
Recently, the Smith-Waterman algorithm has been successfully mapped onto the emerging general-purpose graphics processing units (GPUs).
In this paper, we focused on how to improve the mapping, especially for short query sequences, by better usage of shared memory.
We performed and evaluated the proposed method on two different platforms (Tesla C1060 and Tesla K20) and compared it with two classic methods in CUDASW++.
Further, the performance on different numbers of threads and blocks has been analyzed.
The results showed that the proposed method significantly improves Smith-Waterman algorithm on CUDA-enabled GPUs in proper allocation of block and thread numbers.
American Psychological Association (APA)
Huang, Liang-Tsung& Wu, Chao-Chin& Lai, Lien-Fu& Li, Yun-Ju. 2015. Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs. BioMed Research International،Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1054540
Modern Language Association (MLA)
Huang, Liang-Tsung…[et al.]. Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs. BioMed Research International No. 2015 (2015), pp.1-10.
https://search.emarefa.net/detail/BIM-1054540
American Medical Association (AMA)
Huang, Liang-Tsung& Wu, Chao-Chin& Lai, Lien-Fu& Li, Yun-Ju. Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs. BioMed Research International. 2015. Vol. 2015, no. 2015, pp.1-10.
https://search.emarefa.net/detail/BIM-1054540
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1054540