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Nucleic Acids Research 2005 33(Web Server Issue):W489-W492; doi:10.1093/nar/gki358
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

SNP Cutter: a comprehensive tool for SNP PCR–RFLP assay design

Ruifang Zhang1, Zanhua Zhu1, Hongming Zhu2, Tu Nguyen2, Fengxia Yao1, Kun Xia1, Desheng Liang1 and Chunyu Liu1,2,*

1National Laboratory of Medical Genetics of China, Central South University Changsha, Hunan, People's Republic of China 2Department of Psychiatry, University of Chicago Chicago, IL, USA

*To whom correspondence should be addressed at R022, BSLC, 924 E. 57th Street, Department of Psychiatry, University of Chicago, IL 60637, USA. Tel: +1 773 834 3604; Fax: +1 773 834 2970; Email: cliu{at}yoda.bsd.uchicago.edu

Received February 3, 2005. Accepted February 7, 2005.

The Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) is a relatively simple and inexpensive method for genotyping single nucleotide polymorphisms (SNPs). It requires minimal investment in instrumentation. Here, we describe a web application, ‘SNP Cutter,’ which designs PCR–RFLP assays on a batch of SNPs from the human genome. NCBI dbSNP rs IDs or formatted SNPs are submitted into the SNP Cutter which then uses restriction enzymes from a pre-selected list to perform enzyme selection. The program is capable of designing primers for either natural PCR–RFLP or mismatch PCR–RFLP, depending on the SNP sequence data. SNP Cutter generates the information needed to evaluate and perform genotyping experiments, including a PCR primers list, sizes of original amplicons and different allelic fragment after enzyme digestion. Some output data is tab-delimited, therefore suitable for database archiving. The SNP Cut-ter is available at http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm.


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