ABSTRACT
PCR-CTPP (Polymerase Chain Reaction with Confronting Two-Pair Primers) is a simple, fast and economical biotechnology for SNP (Single Nucleotide Polymorphism) genotyping. Although many SNPs have been successfully genotyped by PCR-CTPP, computation methods for screen feasible CTPP primers are still challenging. The main difficult is many constraint factors must be simultaneously considered in four primers and the melting temperatures among primers must be highly close. Recently, a GA (Genetic Algorithm)-based method had been developed to solve the problem of screening PCR-CTPP primers. However, the shortcoming of the GA for easily be trapped makes it regularly fail to find feasible CTPP primers. In this study, our aim is to improve the GA based on integrating local search mechanism into the GA. Flanking sequences in 500 bps for SNP IDs rs62068666, rs62068667, rs71372212, rs72557980, rs72557981, rs72557982, rs72557983, rs72557984, rs73263853, and rs73263865 involved in the serotonin transporter protein gene SLC6A4 are used to take as template sequences for screen CTPP primers. We compare the results to those of the original GA method, and we find that the local search mechanism is helpful for screening more feasible CTPP primers.
