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题名: An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model
作者: Li, M ;  Ou-Yang, ZC
刊名: THIN SOLID FILMS
出版日期: 2006
卷号: 499, 期号:40910, 页码:207-212
关键词: I SENSITIVITY ;  INVIVO ;  SUPERCOILS ;  GENES
学科分类: Physics
通讯作者: Li, M , Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China
部门归属: Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China; Tsing Hua Univ, Ctr Adv Study, Beijing 100084, Peoples R China
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.
收录类别: SCI
原文出处: 查看原文
WOS记录号: WOS:000235826500038
Citation statistics: 
内容类型: 期刊论文
URI标识: http://ir.itp.ac.cn/handle/311006/6018
Appears in Collections:理论物理所1978-2010年知识产出_期刊论文

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Recommended Citation:
Li, M,Ou-Yang, ZC. An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model[J]. THIN SOLID FILMS,2006,499(40910):207-212.
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