| An exact numerical method to calculate the base-unpairing probability for any given DNA sequence by Benham model | |
| Li, M ; Ou-Yang, ZC | |
| 2010-05-06 ; 2010-05-06 | |
| 会议名称 | THIN SOLID FILMS ; 6th Intrernational Conference on Nano-Molecular Electronics (ICNME2004) ; Kobe, JAPAN ; Web of Science |
| 关键词 | dsDNA unwinding local denaturation generating function I SENSITIVITY INVIVO SUPERCOILS GENES Materials Science, Multidisciplinary Materials Science, Coatings & Films Physics, Applied Physics, Condensed Matter |
| 中文摘要 | 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. |
| 会议录出版者 | ELSEVIER SCIENCE SA ; LAUSANNE ; PO BOX 564, 1001 LAUSANNE, SWITZERLAND |
| 语种 | 英语 ; 英语 |
| 内容类型 | 会议论文 |
| 源URL | [http://hdl.handle.net/123456789/6880]  |
| 专题 | 清华大学 |
| 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:THIN SOLID FILMS, 6th Intrernational Conference on Nano-Molecular Electronics (ICNME2004), Kobe, JAPAN, Web of Science. |
| 个性服务 |
| 查看访问统计 |
| 相关权益政策 |
| 暂无数据 |
| 收藏/分享 |
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。
修改评论