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LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs  

2011-05-12 15:43:09|  分类: GWAS |  标签: |举报 |字号 订阅

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Hsueh-Wei Chang1,2,3 email, Li-Yeh Chuang4 email, Yan-Jhu Chang6 email, Yu-Huei Cheng6 email, Yu-Chen Hung1 email, Hsiang-Chi Chen5 email and Cheng-Hong Yang6 email

1  Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan

2  Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan

3  Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan

4  Department of Chemical Engineering, I-Shou University, Kaohsiung, Taiwan

5  Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan

6  Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan

LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs - 喜欢吃桃子 - wangyufeng的博客 author emailLD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs - 喜欢吃桃子 - wangyufeng的博客 corresponding author email

BMC Genetics 2009, 10:26doi:10.1186/1471-2156-10-26

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2156/10/26

Received: 11 November 2008
Accepted: 6 June 2009
Published: 6 June 2009

? 2009 Chang et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Abstract
Background
Linkage disequilibrium (LD) mapping is commonly used to evaluate markers for genome-wide association studies. Most types of LD software focus strictly on LD analysis and visualization, but lack supporting services for genotyping.


Results
We developed a freeware called LD2SNPing, which provides a complete package of mining tools for genotyping and LD analysis environments. The software provides SNP ID- and gene-centric online retrievals for SNP information and tag SNP selection from dbSNP/NCBI and HapMap, respectively. Restriction fragment length polymorphism (RFLP) enzyme information for SNP genotype is available to all SNP IDs and tag SNPs. Single and multiple SNP inputs are possible in order to perform LD analysis by online retrieval from HapMap and NCBI. An LD statistics section provides D, D', r2, δQ, ρ, and the P values of the Hardy-Weinberg Equilibrium for each SNP marker, and Chi-square and likelihood-ratio tests for the pair-wise association of two SNPs in LD calculation. Finally, 2D and 3D plots, as well as plain-text output of the results, can be selected.
Conclusion
LD2SNPing thus provides a novel visualization environment for multiple SNP input, which facilitates SNP association studies. The software, user manual, and tutorial are freely available at http://bio.kuas.edu.tw/LD2NPing webcite.


Additional File 1. User manual for LD2SNPing. User manual for LD2SNPing.

Format: PDF Size: 12.8MB Download file

This file can be viewed with: Adobe Acrobat Reader


LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs - 喜欢吃桃子 - wangyufeng的博客 more information pls links to:http://www.biomedcentral.com/1471-2156/10/26 LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs - 喜欢吃桃子 - wangyufeng的博客

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