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- Title
SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design.
- Authors
Zhang, Ruifang; Zhu, Zanhua; Zhu, Hongming; Nguyen, Tu; Yao, Fengxia; Xia, Kun; Liang, Desheng; Liu, Chunyu
- Abstract
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.
- Publication
Nucleic acids research, 2005, Vol 33, Issue Web Server issue, pW489
- ISSN
1362-4962
- Publication type
Journal Article
- DOI
10.1093/nar/gki358