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SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.
Lin Wang1, Simin Liu, Tianhua Niu
1Program for Population Genetics, Harvard School of Public Health, Boston, MA 02115, USA. linwang@hsph.harvard.edu
BMC Bioinformatics
|March 19, 2005
Summary
SNPHunter is a new software tool that simplifies finding and selecting single nucleotide polymorphisms (SNPs) for genetic studies. It efficiently screens and retrieves SNP data, aiding complex disease research.
Area of Science:
- Genetics and Bioinformatics
- Molecular Evolution
Background:
- Single nucleotide polymorphisms (SNPs) are crucial for identifying disease susceptibility genes and understanding human evolution.
- Selecting optimal SNP sets from databases is a major challenge for large-scale genetic studies, especially in case-control designs.
Purpose of the Study:
- To introduce SNPHunter, a novel software program designed to streamline the process of SNP selection and data retrieval.
- To provide a user-friendly tool for both ad hoc and batch-mode SNP searching and filtering.
Main Methods:
- SNPHunter allows searching and filtering of SNP data from NCBI dbSNP.
- It retrieves comprehensive SNP information including physical position, function class, flanking sequences, and heterozygosity.
- Extracted SNP data can be exported in plain text format for downstream analyses.
Main Results:
- The SNPHunter software facilitates efficient SNP screening, selection, and acquisition.
- The tool was successfully applied to select SNPs for 10 major type 2 diabetes candidate genes.
- The software offers both ad hoc and batch processing modes for SNP data management.
Conclusions:
- SNPHunter is an efficient and user-friendly tool for SNP analysis.
- The software simplifies the process of acquiring and utilizing SNP data for genetic research.
- The tool is available for download along with a user's manual.