A Method for Degenerate Primer Design Based on Artificial Bee Colony Algorithm

Abstract

Aiming to address the complex degenerate primer design problem in the biological field, in this paper, we design a degenerate primer optimization model considering primer coverage and degeneracy that allows a small number of base mismatches, and propose a global optimization method based on the artificial bee colony algorithm. The proposed algorithm combines the idea of the ant colony algorithm with the optimization process of the artificial bee colony algorithm, overcomes the disadvantage of the uncertain candidate solution length of the artificial bee colony algorithm in solving discrete optimization problems, designs the search space model according to the construction process of candidate solution in ant colony optimization algorithm, and redesigns various bee foraging strategies according to the optimization process information. In the comparative experiments on DNA template sequences of different scales, the degenerate primer designed by the proposed algorithm is superior to the existing methods in terms of stability, specificity, coverage and degeneracy.