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SNPCheck is a bioinformatic program designed to check oligonucleotide primers for common Single Nucleotide Polymorphisms (SNPs). This tool provides an important safety check in the standard primer design process, enabling scientists to identify SNPs that could cause instability in primer hybridisation during PCR and lead to inaccurate sequencing results, which in the clinical setting could lead to errors in patient diagnosis.
Data on common Single Nucleotide Polymorphisms (SNPs) can be found in a number of publically available databases and datasets, such as dbSNP, 1000 Genomes Project and Exome Sequencing Project. However, the analysis needed to locate possible SNPs in the hundreds of primers used by laboratories is impractical without a bioinformatic pipeline like SNPCheck.
SNPCheck uses the latest build of the human genome from NCBI, and BLAST to identify the position in the sequence where the primers bind. The contents of the current release of dbSNP, 1000 Genomes Project and ESP are used to identify if there are any known SNPs at the primer binding sites.
Subscription to SNPCheck provides access to the batch check facility as well as personalised laboratory profiles with features such as primer storage and saved results. Single primer pairs can be checked without a subscription. More information about subscription and pricing can be found here.