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An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model
Li, M; Ou-Yang, ZC; Li, M , Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China
2006
发表期刊THIN SOLID FILMS
ISSN0040-6090
卷号499期号:40910页码:207-212
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.
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
关键词i Sensitivity Invivo Supercoils Genes
学科领域Physics
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收录类别SCI
WOS记录号WOS:000235826500038
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被引频次:1[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/6018
专题1978-2010年知识产出
通讯作者Li, M , Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China
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Li, M,Ou-Yang, ZC,Li, M , Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China. 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.
APA Li, M,Ou-Yang, ZC,&Li, M , Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China.(2006).An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model.THIN SOLID FILMS,499(40910),207-212.
MLA Li, M,et al."An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model".THIN SOLID FILMS 499.40910(2006):207-212.
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