Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype
文献类型：期刊论文
| 作者 | Zhang, Xiang-Sun2 ; Wang, Rui-Sheng1; Wu, Ling-Yun2; Zhang, Wei3
|
| 刊名 | EVOLUTIONARY BIOINFORMATICS
 |
| 出版日期 | 2006 |
| 卷号 | 2页码:261-270 |
| 关键词 | individual haplotyping minimum conflict individual haplotyping NP-hard dynamic programming feed-forward neural network reconstruction rate |
| ISSN号 | 1176-9343 |
| 英文摘要 | The Minimum Error Correction (MEC) is an important model for haplotype reconstruction from SNP fragments. However, this model is effective only when the error rate of SNP fragments is low. In this paper, we propose a new computational model called Minimum Conflict Individual Haplotyping (MCIH) as an extension to MEC. In contrast to the conventional approaches, the new model employs SNP fragment information and also related genotype information, thereby a high accurate inference can be expected. We first prove the MCIH problem to be NP-hard. To evaluate the practicality of the new model we design an exact algorithm (a dynamic programming procedure) to implement MCIH on a special data structure. The numerical experience indicates that it is fairly effective to use MCIH at the cost of related genotype information, especially in the case of SNP fragments with a high error rate. Moreover, we present a feed-forward neural network algorithm to solve MCIH for general data structure and large size instances. Numerical results on real biological data and simulation data show that the algorithm works well and MCIH is a potential alternative in individual haplotyping. |
| 资助项目 | National Natural Science Foundation of China[10471141] ; National Natural Science Foundation of China[60503004] ; Some Important Problems in Bioinformatics, CAS, China ; Kyoto University, Japan ; Research Fund of School of Information, Renmin University of China |
| WOS研究方向 | Evolutionary Biology ; Mathematical & Computational Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:000205733800023 |
| 出版者 | BIOINFORMATICS INST |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/3716]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Wang, Rui-Sheng |
| 作者单位 | 1.Renmin Univ China, Sch Informat, Beijing 100872, Peoples R China 2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 3.N Carolina State Univ, Raleigh, NC 27695 USA |
| 推荐引用方式 GB/T 7714 | Zhang, Xiang-Sun,Wang, Rui-Sheng,Wu, Ling-Yun,et al. Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype[J]. EVOLUTIONARY BIOINFORMATICS,2006,2:261-270. |
| APA | Zhang, Xiang-Sun,Wang, Rui-Sheng,Wu, Ling-Yun,&Zhang, Wei.(2006).Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype.EVOLUTIONARY BIOINFORMATICS,2,261-270. |
| MLA | Zhang, Xiang-Sun,et al."Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype".EVOLUTIONARY BIOINFORMATICS 2(2006):261-270. |
入库方式： OAI收割
来源：数学与系统科学研究院
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