Function Minimization In DNA Sequence Design Based On Binary Particle Swarm Optimization

In DNA based computation and DNA nanotechnology, the design of good DNAsequences has turned out to be an elementary problem and one of the most practical andimportant research topics. Although the design of DNA sequences is dependent on the protocolof biological experiments, it is highly required to establish a method for the systematic design ofDNA sequences, which could be applied to various design constraints. Basically, the fitness ofDNA sequences can be evaluated using four objective functions, namely, similarity, H measure,continuity, and hairpin. In this paper, binary particle swarm optimization (BinPSO) is proposedto minimize those objective functions individually, subjected to two constraints: meltingtemperature and GC content. An implementation of the optimization process is presented using 20particles and the results obtained shows the correctness of PSO computation, where theminimized values for each objective can be achieved.