Primer design with specific PCR product size using Memetic algorithm

In order to provide feasible primer set for performing a polymerase chain reaction (PCR) experiment, many primer design methods have been proposed. However, the majority of these methods require a long time to obtain an optimal solution since quantities of template DNA need to be analyzed, and the designed primer sets usually do not provide a specific PCR product size. Evolutionary computation has been applied to PCR primer design and appeared to yield good results. In this paper, a memetic algorithm is proposed to solve primer design problems associated with providing a specific product size for PCR experiments. A simple accuracy for the primer design of the gene CYP1A1, associated with a heightened lung cancer risk, calculated and the sequence NM_000499. Five hundred runs of MA and GA primer design methods were performed with different PCR product lengths, and with different methods of calculating Tm ways are performed. A comparison of the accuracy results for GA and MA primer design showed that the MA for primer design yields better than the GA for primer design. The results further indicated that the proposed method finds optimal or near-optimal primer sets and effective PCR products from a large amount of template DNA in a relatively short time.