SNPHunter

SNPHunter facilitates search, selection, and management of single nucleotide polymorphisms (SNPs) for genetic studies, enabling SNP retrieval and filtering for linkage disequilibrium and association analyses.

Key Features:

• Ad Hoc and Batch-Mode SNP Search: Performs both individual (ad hoc) and large-scale batch-mode queries for SNP retrieval.
• Automatic SNP Filtering: Applies automatic filtering mechanisms to refine SNP lists according to specified criteria.
• Comprehensive Data Retrieval from NCBI dbSNP: Retrieves physical position, function class, flanking sequences with user-defined lengths, and heterozygosity measures from NCBI dbSNP.
• Data Export in Plain Text: Exports retrieved SNP information in plain text format for downstream analyses.

Scientific Applications:

• Linkage Disequilibrium Study Design: Supports design of large-scale linkage disequilibrium studies, including case-control settings.
• Candidate-Gene SNP Selection for Complex Disease Studies: Enables selection of SNPs from candidate genes for complex diseases, exemplified by selection from CAPN10, FABP4, IL6, NOS3, PPARG, TNF, UCP2, CRP, ESR1, and AR in type 2 diabetes research.

Methodology:

The software performs ad hoc and batch-mode queries against NCBI dbSNP, retrieves SNP attributes (physical position, function class, flanking sequences, heterozygosity), applies filtering criteria to refine results, and exports data in plain text.