A Degenerate Primer Design Method Based on Ant Colony Optimization

Abstract

For the existed biological degenerate primer design problem, a solution method based on an ant colony optimization algorithm is proposed, in which an optimization model considers primer coverage as well as degeneracy while allowing for a small number of base mismatches. Using the construction graph model, the algorithm makes full use of the dynamic change information during the iterative optimal path optimization process, strengthens the explored new path pheromone, and selects the primers that meet the constraints. The results of DNA template sequence matching experiments show that the degenerate primers designed by the proposed algorithm outperform existing approaches.