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LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs
Hsueh-Wei Chang1, Li-Yeh Chuang, Yan-Jhu Chang
1Department of Chemical Engineering, I-Shou University, Kaohsiung, Taiwan. chuang@isu.edu.tw
BMC Genetics
|June 9, 2009
Summary
LD2SNPing is a freeware tool that integrates genotyping and linkage disequilibrium (LD) analysis for genome-wide association studies. It offers comprehensive data retrieval, LD statistics, and visualization for SNP association studies.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Linkage disequilibrium (LD) mapping is crucial for genome-wide association studies.
- Existing LD software often lacks integrated genotyping functionalities.
Purpose of the Study:
- To develop a comprehensive freeware tool, LD2SNPing, for integrated genotyping and LD analysis.
- To enhance SNP association studies through improved data mining and visualization.
Main Methods:
- Developed LD2SNPing freeware with online retrieval from dbSNP/NCBI and HapMap.
- Integrated SNP ID and gene-centric information retrieval and tag SNP selection.
- Included RFLP enzyme information and support for single/multiple SNP inputs for LD analysis.
Main Results:
- LD2SNPing provides a complete package for genotyping and LD analysis.
- Offers various LD statistics (D, D', r2, deltaQ, rho) and Hardy-Weinberg Equilibrium tests.
- Features 2D/3D plots and plain-text output for results visualization.
Conclusions:
- LD2SNPing offers a novel visualization environment for multiple SNP inputs, aiding SNP association studies.
- The software, manual, and tutorial are freely available for academic use.
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