SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design.
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.
Zhang
Ruifang
R
National Laboratory of Medical Genetics of China, Central South University Changsha, Hunan, People's Republic of China.
Zhu
Zanhua
Z
Zhu
Hongming
H
Nguyen
Tu
T
Yao
Fengxia
F
Xia
Kun
K
Liang
Desheng
D
Liu
Chunyu
C
D017931:DNA Primers; D004262:DNA Restriction Enzymes; D005838:Genotype; D006801:Humans; D020407:Internet; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D012984:Software; D014584:User-Computer Interface
D017931:DNA Primers; D004262:DNA Restriction Enzymes