An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model

doi:10.1016/j.tsf.2005.07.007

	An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model
	Li, M ; Ou-Yang, ZC
	2006
会议日期	DEC 15-17, 2004
会议地点	Kobe, JAPAN
关键词	I SENSITIVITY INVIVO SUPERCOILS GENES
卷号	499
期号	1-2
DOI	10.1016/j.tsf.2005.07.007
页码	207-212
英文摘要	In this article we report an exact numerical method to calculate the partition function of Benham model which describes the stress-induced denaturation of cloublestrand DNA (dsDNA). Generating function approach is employed in the algorithm. It successes to avoid the catastrophic sign cancellation which makes Benham's algorithm impractical to analyze DNA sequences longer than 10 kb. By our algorithm, the transition profile of base-unpairing probability can be efficiently computed for very long sequences on PC (32-bit, CPU frequency 1.4 GHz). The algorithm requires O(N-3) operations and O(Nlog(2)N) memory, and by contrast Benham's algorithm needs O(N(3)log(2)N) operations and O(N-2) memory. Examples are given on the performance of the implementation on single CPU and multi-CPU cluster. (c) 2005 Elsevier B.V All rights reserved.
会议录	THIN SOLID FILMS
会议录出版者	ELSEVIER SCIENCE SA
会议录出版地	LAUSANNE
语种	英语
URL标识	查看原文
ISSN号	0040-6090
WOS研究方向	Materials Science ; Physics
内容类型	会议论文
源URL	[http://ir.itp.ac.cn/handle/311006/23691]
专题	SCI会议论文
作者单位	1.Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China 2.Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China
推荐引用方式 GB/T 7714	Li, M,Ou-Yang, ZC. An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model[C]. 见:. Kobe, JAPAN. DEC 15-17, 2004.