SNPCheck

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Data on common Single Nucleotide Polymorphisms (SNPs) is freely available in dbSNP, but the analysis needed to locate possible SNPs in the hundreds of primers used by laboratories is impractical without a bioinformatic pipeline.

 

Diagnostic SNPCheck is a bioinformatic program for the UK diagnostic community launched by NGRL Manchester in 2005 for batch checking of oligonucleotide primers for SNPs. It 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 is used to identify if there are any known SNPs at the primer binding sites.

 

Up until the end of September 2009, SNPCheck v1 had been used to test over 270,000 primers for SNPs. A user evaluation in 2007 was highly positive, showing that SNPCheck has become an essential tool for laboratories, some of which have included the application in their Standard Operating Procedures.

 

The updated and improved SNPCheck v2.0 application was launched in August 2009, and is regularly used to test between two and four thousand  batches per month. This can constitute up to 30,000 primer pairs tested  in a month.

We aim to, at least, maintain current levels of usage throughout the project and update the application within one week of each new dbSNP dataset release.

 

Mailing List - Keep up to date with new SNPs

 

Users of Diagnostic SNPCheck can sign up to a mailing list to receive updates on new releases of dbSNP, the human genome and the SNPCheck software itself. By signing up you will know exactly when the checks you have done on your primers have become out of date. To subscribe to the mailing list send an email with "subscribe snpcheck" in the message body to LISTSERV@listserv.manchester.ac.uk