Single Nucleotide Polymorphism (SNP) Explorer

Analysis and visualization of hyper-igm/cvid re-sequencing microarray data

Benefits and Features

  • Simple analysis for large amounts of re-sequencing chip data: all of the steps needed for identification of SNPs are automated, including mapping, alignment, and comparison steps
  • Web-based application
    • No need to download multiple analysis tools and databases
    • Simply upload raw data files and start the automated workflow
  • Graphical interface for easy evaluation of novel SNPs include pop-up windows with detailed information about each SNP, sorting options that allow quick selection of specific features, and summary tables for each type of SNP data

Access the software.


SNP Explorer is a web-based application used for the visualization and analysis of SNPs from custom Affymetrix resequencing Hyper-IgM/CVID microarrays. The application helps in the high-throughput discovery of novel mutations among hundreds of disease-relevant genes in patients with Hyper-IgM/CVID or other primary immunodeficiency diseases.


This software is provided free of charge by NIAID.


The web interface of SNP Explorer was developed using the latest BioGraphics Perl library. The gene and the known SNP information were extracted from UCSC genome database annotations. With further development, the SNP Explorer framework can be adapted for processing any resequencing array data.

Content last reviewed on March 20, 2012