PCR-CTPP Design for Enzyme-Free SNP Genotyping Using Memetic Algorithm
Lately, several single nucleotide polymorphisms (SNPs) have been successfully genotyped by polymerase chain reaction with confronting 2-try primers (PCR-CTPP). However, computation experiments of possible CTPP primers are still challenging. The melting temperatures between four primers should be within a terribly slender range, and several primer constraints want to be conformed to. PCR-CTPP could be a simple, time- and value-effective SNP genotyping methodology applied in molecular biology and biomedical fields. In this study, an MA (memetic algorithm)-based mostly method is proposed to enable the design of possible CTPP primer sets. Overall, 28eight SNPs which exclude the deletion/insertion polymorphisms (DIPs) and multi-nucleotide polymorphisms (MNPs) in the SLC6A4 gene were tested in silico. The results were compared with a GA (genetic algorithm)-primarily based methodology and indicate that the proposed technique provides more possible CTPP primers than the GA-based method. The MA-based CTPP primer style method provides crucial melting temperatures and all sorts of evaluation of the common primer constraints. It could conceivably assist biologists and alternative researchers in getting feasible CTTP primer sets. The MA-CTPP algorithm is implemented in Java and a user-friendly input interface is freely available at http://bio.kuas.edu.tw/ma-ctpp/.
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