An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model
文献类型：期刊论文
| 作者 | Ou-Yang, ZC ; Li, M; Li, M , Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China
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| 刊名 | THIN SOLID FILMS
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| 出版日期 | 2006 |
| 卷号 | 499期号:40910页码:207-212 |
| 关键词 | i Sensitivity Invivo Supercoils Genes |
| ISSN号 | 0040-6090 |
| 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. |
| 学科主题 | Physics |
| URL标识 | 查看原文 |
| WOS记录号 | WOS:000235826500038 |
| 公开日期 | 2012-08-02 |
| 源URL | [http://ir.itp.ac.cn/handle/311006/6018]  |
| 专题 | 理论物理研究所_理论物理所1978-2010年知识产出 |
| 通讯作者 | Li, M , Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China |
| 推荐引用方式 GB/T 7714 | Ou-Yang, ZC,Li, M,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 | Ou-Yang, ZC,Li, M,&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 | Ou-Yang, ZC,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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来源：理论物理研究所
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