A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms

doi:10.1007/s11265-007-0073-6

	A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms
	Lavenier, D.; Georges, G.; Liu, X.
	2007-09-01
发表期刊	JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY
ISSN	0922-5773
卷号	48 期号:3 页码:255-269
摘要	Genomic sequence comparison algorithms represent the basic toolbox for processing large volume of DNA or protein sequences. They are involved both in the systematic scan of databases, mostly for detecting similarities with an unknown sequence, and in preliminary processing before advanced bioinformatics analysis. Due to the exponential growth of genomic data, new solutions are required to keep the computation time reasonable. This paper presents a specific hardware architecture to speed-up seed-based algorithms which are currently the most popular heuristics for detecting alignments. The architecture regroups FLASH and FPGA technologies on a common support, allowing a large amount of data to be rapidly accessed and quickly processed. Experiments on database search and intensive sequence comparison demonstrate a good cost/performance ratio compared to standard approaches.
关键词	bioinformatics genomics sequence comparison reconfigurable architecture FLASH memory index indexing seed-based algorithm
DOI	10.1007/s11265-007-0073-6
收录类别	SCI
语种	英语
WOS研究方向	Computer Science ; Engineering
WOS类目	Computer Science, Information Systems ; Engineering, Electrical & Electronic
WOS记录号	WOS:000249211900006
出版者	SPRINGER
引用统计	被引频次：10[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/2XEOYT63/10919
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Lavenier, D.
作者单位	1.INRISA CNRS, F-35042 Rennes, France 2.CAS, Comp Technol Inst, Key Lab Comp Syst & Architect, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Lavenier, D.,Georges, G.,Liu, X.. A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms[J]. JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY,2007,48(3):255-269.
APA	Lavenier, D.,Georges, G.,&Liu, X..(2007).A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms.JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY,48(3),255-269.
MLA	Lavenier, D.,et al."A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms".JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY 48.3(2007):255-269.