An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model
文献类型：会议论文
| 作者 | Li, M ; Ou-Yang, ZC
|
| 出版日期 | 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 |
| 源URL | [http://ir.itp.ac.cn/handle/311006/23691]  |
| 专题 | SCI会议论文 |
| 作者单位 | 1.Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China 2.Tsing Hua Univ, Ctr Adv Study, Beijing 100084, 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. |
入库方式： OAI收割
来源：理论物理研究所
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