Haplotype reconstruction from SNP fragments by minimum error correction

doi:10.1093/bioinformatics/bti352

CSpace > 应用数学研究所

	Haplotype reconstruction from SNP fragments by minimum error correction
	Wang, RS ; Wu, LY; Li, ZP ; Zhang, XS
	2005-05-15
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	21 期号:10 页码:2456-2462
摘要	Motivation: Haplotype reconstruction based on aligned single nucleotide polymorphism (SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. An important computational model of this problem is the minimum error correction (MEC) model, which has been mentioned in several literatures. The model retrieves a pair of haplotypes by correcting minimum number of SNPs in given genome fragments coming from an individual's DNA. Results: In the first part of this paper, an exact algorithm for the MEC model is presented. Owing to the NP-hardness of the MEC model, we also design a genetic algorithm (GA). The designed GA is intended to solve large size problems and has very good performance. The strength and weakness of the MEC model are shown using experimental results on real data and simulation data. In the second part of this paper, to improve the MEC model for haplotype reconstruction, a new computational model is proposed, which simultaneously employs genotype information of an individual in the process of SNP correction, and is called MEC with genotype information (shortly, MEC/GI). Computational results on extensive datasets show that the new model has much higher accuracy in haplotype reconstruction than the pure MEC model.
DOI	10.1093/bioinformatics/bti352
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000229285600040
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/2187
专题	应用数学研究所
通讯作者	Wang, RS
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 2.Beijing Mat Inst, Beijing 101149, Peoples R China
推荐引用方式 GB/T 7714	Wang, RS,Wu, LY,Li, ZP,et al. Haplotype reconstruction from SNP fragments by minimum error correction[J]. BIOINFORMATICS,2005,21(10):2456-2462.
APA	Wang, RS,Wu, LY,Li, ZP,&Zhang, XS.(2005).Haplotype reconstruction from SNP fragments by minimum error correction.BIOINFORMATICS,21(10),2456-2462.
MLA	Wang, RS,et al."Haplotype reconstruction from SNP fragments by minimum error correction".BIOINFORMATICS 21.10(2005):2456-2462.