Fuzzy adaptive particle swarm optimization for a specific primer design problem

A fuzzy system with dynamically adapt the inertia weight of the particle swarm optimization (FAPSO) had been implemented to select a specific feasible primer pair for PCR experiments. Overall, fifty accession nucleotide sequences between 1900 bps and 2100 bps were sampled for primer design with specific PCR product lengths of 150~300 bps and 500~800 bps. Total five hundred runs of the proposed primer design approaches were performed for each accession nucleotide sequence to calculate the optimum accuracy. The proposed approach is compared to standard PSO primer design method. The results generated in a dry dock experiment showed that the FAPSO primer design yielded approximately optimal primer sets and had a relatively short CPU-time than standard PSO. Related materials are available online at http://bio.kuas.edu.tw/fapso-pd/.