Abstract
The quality of DNA encoding sequences will not only directly affect the efficiency of DNA computing but also determine the reliability of the biology process. So the ideal encoding sequence design in DNA computing is one of the core issues. Because the design is a complex nonlinear constrained optimization problem, so a new Artificial Fish Swarm Algorithm (AFSA) can be applied to the optimization of the DNA encoding sequences. A constraint handling strategy suit for AFSA is proposed and an improved AFSA is presented by adjusting the parameter automatically in basic AFSA to enhance the search capability of the algorithm in the local area for the encoding sequence design. The simulation results show that the algorithm can improve the quality of encoding sequences while reducing search time.
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