Primer Design Using Gravitational Search Algorithm

Proper primer design is actually one of the most important factors/steps in successful DNA sequencing. There are many constraints that should be satisfied for designing theoptimal primers. In recent years, many methods have been proposed to provide feasible primer set. But designed primer setsby these methods usually do not provide a specific PCR product. Moreover, this process takes a long time. Today, for obtaining approved solutions, evolutionary Algorithms have been applied to the primer design problem. This paper presents a primer design method based on Gravitational Search Algorithm (GSA).GSA is a recently proposed optimization algorithm that is applied for many problems. For valid comparison, the geneCYP1A has been selected that is frequently used in previous researches. This gene is associated with a heightened lung cancerrisk. Analyzing of the results confirms that the accuracy, time efficiency and reliability of GSA based method are better than PSO based method.

Keywords:

component , PCR , primer design , gravitational search algorithm , optimization