Haplo2Ped: a tool using haplotypes as markers for linkage analysis

doi:10.1186/1471-2105-12-350

CORC > 中国农业科学院 > 蔬菜花卉研究所

	Haplo2Ped: a tool using haplotypes as markers for linkage analysis
	Cheng, Feng 1,2; Zhang, Xianglong 1,3; Zhang, Yinan 1; Li, Chaohua 1; Zeng, Changqing 1
刊名	BMC BIOINFORMATICS
	2011
卷号	12 页码:-
ISSN号	1471-2105
DOI	10.1186/1471-2105-12-350
通讯作者	Cheng, Feng
英文摘要	Background: Generally, SNPs are abundant in the genome; however, they display low power in linkage analysis because of their limited heterozygosity. Haplotype markers, on the other hand, which are composed of many SNPs, greatly increase heterozygosity and have superiority in linkage statistics.Results: Here we developed Haplo2Ped to automatically transform SNP data into haplotype markers and then to compute the logarithm (base 10) of odds (LOD) scores of regional haplotypes that are homozygous within the disease co-segregation haploid group. The results are reported as a hypertext file and a 3D figure to help users to obtain the candidate linkage regions. The hypertext file contains parameters of the disease linked regions, candidate genes, and their links to public databases. The 3D figure clearly displays the linkage signals in each chromosome. We tested Haplo2Ped in a simulated SNP dataset and also applied it to data from a real study. It successfully and accurately located the causative genomic regions. Comparison of Haplo2Ped with other existing software for linkage analysis further indicated the high effectiveness of this software.Conclusions: Haplo2Ped uses haplotype fragments as mapping markers in whole genome linkage analysis. The advantages of Haplo2Ped over other existing software include straightforward output files, increased accuracy and superior ability to deal with pedigrees showing incomplete penetrance. Haplo2Ped is freely available at: http://bighapmap.big.ac.cn/software.html.
学科主题	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology ; BIOCHEMICAL RESEARCH METHODS ; BIOTECHNOLOGY & APPLIED MICROBIOLOGY ; MATHEMATICAL & COMPUTATIONAL BIOLOGY
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000295225000001
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/101950]
专题	蔬菜花卉研究所
作者单位	1.Chinese Acad Sci, Beijing Inst Genom, Lab Dis Genom & Individualized Med, Beijing 100029, Peoples R China 2.Chinese Acad Agr Sci, Inst Vegetables & Flowers, Beijing 100081, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Cheng, Feng,Zhang, Xianglong,Zhang, Yinan,et al. Haplo2Ped: a tool using haplotypes as markers for linkage analysis[J]. BMC BIOINFORMATICS,2011,12:-.
APA	Cheng, Feng,Zhang, Xianglong,Zhang, Yinan,Li, Chaohua,&Zeng, Changqing.(2011).Haplo2Ped: a tool using haplotypes as markers for linkage analysis.BMC BIOINFORMATICS,12,-.
MLA	Cheng, Feng,et al."Haplo2Ped: a tool using haplotypes as markers for linkage analysis".BMC BIOINFORMATICS 12(2011):-.