An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors
文献类型：期刊论文
| 作者 | Zhang, Ji-Hong; Wu, Ling-Yun ; Zhao, Yu-Ying; Zhang, Xiang-Sun
|
| 刊名 | EUROPEAN JOURNAL OF OPERATIONAL RESEARCH
 |
| 出版日期 | 2007-10-01 |
| 卷号 | 182期号:1页码:413-427 |
| 关键词 | positional sequencing by hybridization reconstruction of DNA fragment positive errors and negative errors dynamic programming branch and bound algorithm |
| ISSN号 | 0377-2217 |
| DOI | 10.1016/j.ejor.2006.08.031 |
| 英文摘要 | Positional DNA sequencing by hybridization (PSBH) is a recently proposed enhancement of DNA sequencing by hybridization (SBH, potentially a powerful alternative to the DNA sequencing by gel electrophoresis). It has been discussed in many papers and applied to large scale sequencing by hybridization. However, the computational part of PSBH reconstruction is a difficult problem, especially for the occurrence of hybridization errors. So far the problem has not been solved well. Taking PSBH as a combinatorial optimization problem, a novel reconstruction approach to PSBH is presented in this paper. The proposed approach accepts both the negative and positive errors and can greatly reduce ambiguities in the reconstruction of PSBH. The computational experiment shows that our algorithm works satisfactorily and correctly on the test data, especially for the positive errors and k-tuple repetitions. (c) 2006 Elsevier B.V. All rights reserved. |
| WOS研究方向 | Business & Economics ; Operations Research & Management Science |
| 语种 | 英语 |
| WOS记录号 | WOS:000246406000027 |
| 出版者 | ELSEVIER SCIENCE BV |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/4246]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Zhang, Ji-Hong |
| 作者单位 | 1.Tsing Hua Univ, Sch Econ & Managements, Beijing 100084, Peoples R China 2.Chinese Acad Sci, Ctr Bioinformat, Acad Math & Syst Sci, Beijing 100080, Peoples R China 3.Beijing Foreign Studies Univ, Sch Int Business, Beijing 100089, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhang, Ji-Hong,Wu, Ling-Yun,Zhao, Yu-Ying,et al. An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors[J]. EUROPEAN JOURNAL OF OPERATIONAL RESEARCH,2007,182(1):413-427. |
| APA | Zhang, Ji-Hong,Wu, Ling-Yun,Zhao, Yu-Ying,&Zhang, Xiang-Sun.(2007).An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors.EUROPEAN JOURNAL OF OPERATIONAL RESEARCH,182(1),413-427. |
| MLA | Zhang, Ji-Hong,et al."An optimization approach to the reconstruction of positional DNA sequencing by hybridization with errors".EUROPEAN JOURNAL OF OPERATIONAL RESEARCH 182.1(2007):413-427. |
入库方式： OAI收割
来源：数学与系统科学研究院
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