Software

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

Hsueh-Wei Chang^1,2,3 , Li-Yeh Chuang⁴ , Yan-Jhu Chang⁶ , Yu-Huei Cheng⁶ , Yu-Chen Hung¹ , Hsiang-Chi Chen⁵ and Cheng-Hong Yang⁶

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

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

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

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

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

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

author email corresponding author email

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

Published:	6 June 2009

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, δ_Q, 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.