Multiplex PCR primer design for gene family using genetic algorithm

The multiplex PCR experiment is to amplify multiple regions of a DNA sequence at the same time by using different primer pairs. Designing feasible primer pairs for multiplex PCR is a tedious task since there are too many constraints to be satisfied. In this paper, a new method for multiplex PCR primer design strategy using genetic algorithm is proposed. The proposed algorithm is able to find a set of suitable primer pairs more efficient and uses a MAP model to speed up the examination of the specificity constraint that is important for gene family sequences. The dry-dock experiment shows that the proposed algorithm finds several sets of primer pairs of gene family sequences for multiplex PCR that not only obey the design properties, but also have specificity.