Natural SNP-RFLP Primer Design using Memetic Algorithm

Single nucleotide polymorphisms (SNPs) can be genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Before performing PCR-RFLP for SNP genotyping, a feasible primer pair observes numerous constraints and an available restriction enzyme discriminate the target SNP, are required, here we called it natural SNP-RFLP primer design. Design the natural SNP-RFLP primers is usually tedious and challenging problem. In order to get the available primers and restriction enzymes effectively, we use a memetic algorithm (MA) to cooperate with SNP-RFLPing. The test results shown it is able to design feasible primers that fit the common primer constraints and provide the available restriction enzymes.