SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms

Sites in the DNA sequences where two homologous chromosomes differ at a single DNA base are called single nucleotide polymorphisms (SNPs). The human genome contains at least 10 million SNPs, making them the most abundant genetic “lampposts” for pinpointing causal variants underlying human diseases. SNP-related toolboxes and databases have become increasingly important for researchers to choose the most appropriate SNP set for attaining their research goals. This chapter introduces SNPHunter, a web-based software program that allows for SNP search (both ad hoc mode and batch mode), retrieval of SNP information, SNP management, automatic SNP selection based on customizable criteria including physical position, function class, flanking sequences at user-defined lengths, and heterozygosity from National Center for Biotechnology Information dbSNP. The SNP data extracted from dbSNP via SNPHunter can be exported and saved in plain text format for further down-stream analyses.