DNA Computing Sequence Design Based on Bacterial Foraging Algorithm

Abstract

Since the quantity and quality of DNA sequence directly affect the accuracy and efficiency of computation, the design of DNA sequence is critical to DNA computing. In order to improve the reliability of DNA computing, there is a rich literature targeting at making DNA sequences specifically hybridize at a lower melting temperature, no non-complementary bases pairs or mismatch hybridization in the reformed double helix. However, most of them are not good enough to control the melting temperature, because DNA sequence design problem under the constraints of hamming distance, secondary structure, molecular thermodynamic is known to be NP-hard. For the sake of achieving the lower and similar melting temperature for each DNA sequence, we proposed a DNA sequence coding method based on Bacterial Foraging Algorithm (BFA). An evaluation criterion is particularly proposed to assess the quality of DNA sequence in the optimization process. With BFA, high-quality DNA strands are replicated to avoid the participation of inferior strands in the operation. Experiments show our proposed approach significantly outperforms existing methods in terms of continuity and melting temperature.