WASP: a Web-based Allele-Specific PCR assay Designing Tool for Detecting SNPs and Mutations

Researchers from the Biostatistics & Informatics Laboratory, Genome Institute and Mahidol University have successful developed a web-based AS primer design application called WASP for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. This tool can efficiently design AS primers for human SNPs as well as mutations. To guarantee the specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experimental protocols.  In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve their efficiency. 

To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP. This database is tightly integrated with the tool so that users can design primers for existing SNPs without going off the site. Furthermore, WASP offers a graphical user interface through a scalable vector graphic (SVG) drawing tool that allows users to select SNPs and graphically visualize designed primers and their conditions. WASP can be accessed at website: http://bioinfo.biotec.or.th/WASP.  


WASP will be very useful for the study of population genetics, molecular genetics and pharmacogenomics.  The application of such software can be used for diagnosis of genetic diseases in hospitals. This work has recently been published in BMC Genomics 2007 (Vol. 8, no. 275), and has been recognized as a highly accessed article and highlighted on the A-IMBN Research website.


Posted on 31 October 2007.