QuickSNP: an automated web server for selection of tagSNPs

Area of Science:

• Genetics
• Bioinformatics
• Computational Biology

Background:

• Large-scale genetic association studies using single nucleotide polymorphisms (SNPs) are costly.
• Efficient selection of tagSNPs is crucial for maximizing resource utilization in gene mapping.
• Existing SNP selection tools have limitations in cost-effectiveness and feature sets.

Purpose of the Study:

• To develop a cost-effective web server, QuickSNP, for selecting single nucleotide polymorphisms (SNPs).
• To address limitations in existing SNP selection tools and enhance resource utilization for genetic studies.

Main Methods:

• Development of the QuickSNP web server.
• Implementation of automated gene-centric SNP selection from chromosomal regions.
• Inclusion of features for coding non-synonymous SNP selection and SNP filtering based on inter-SNP distances.
• Integration of genotyping assay availability and whole genome chip presence information.

Main Results:

• QuickSNP provides automated selection of gene-centric and coding non-synonymous SNPs.
• The server facilitates SNP filtering based on distance and genotyping assay availability.
• User-friendly summary tables and UCSC Genome Browser tracks are generated for selected tagSNPs.

Conclusions:

• QuickSNP offers a unique combination of features for cost-effective SNP selection.
• The tool is valuable for researchers aiming to select optimal markers for genotyping studies.
• The freely available web server enhances efficiency and resource utilization in genetic research.