A study of architectural optimization methods in bioinformatics applications

doi:10.1177/1094342007078175

	A study of architectural optimization methods in bioinformatics applications
	Tan, G.; Xu, L.; Dai, Z.; Fong, S.; Sun, N.
	2007-09-01
发表期刊	INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
ISSN	1094-3420
卷号	21 期号:3 页码:371-384
摘要	Studies in the optimization of sequence alignment have been carried out in bioinformatics. In this paper, we have focused on two aspects: memory usage and execution time. Our study suggests that cache memory does not have a significant effect on system performance. Our attention then turns to optimize Smith-Waterman's algorithm. Two instruction level methods have been proposed and 2-8 fold speed improvements have been observed after the optimization has been implemented. Further improvements on system performance have been achieved by overlapping computation with system I/O usage.
关键词	bioinformatics sequence alignment cache memory instruction level parallelism I/O overlapping
DOI	10.1177/1094342007078175
收录类别	SCI
语种	英语
WOS研究方向	Computer Science
WOS类目	Computer Science, Hardware & Architecture ; Computer Science, Interdisciplinary Applications ; Computer Science, Theory & Methods
WOS记录号	WOS:000248886900008
出版者	SAGE PUBLICATIONS LTD
引用统计	被引频次：2[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/10850
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Tan, G.
作者单位	Chinese Acad Sci, Inst Comp Technol, Key Lab Comp Syst & Architecture, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Tan, G.,Xu, L.,Dai, Z.,et al. A study of architectural optimization methods in bioinformatics applications[J]. INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS,2007,21(3):371-384.
APA	Tan, G.,Xu, L.,Dai, Z.,Fong, S.,&Sun, N..(2007).A study of architectural optimization methods in bioinformatics applications.INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS,21(3),371-384.
MLA	Tan, G.,et al."A study of architectural optimization methods in bioinformatics applications".INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 21.3(2007):371-384.