Bacterial Foraging Algorithm Based on Activity of Bacteria for DNA Computing Sequence Design

Abstract

Since the quantity and quality of DNA sequence directly affect the accuracy and efficiency of computation, the design of DNA sequence is essential for DNA computing. In order to improve the efficiency and reliability of DNA computing, there is a rich literature targeting at generating DNA sequences with lower similarity that can hybridize at a lower melting temperature. However, it is not trivial to improve both melting temperature and similarity for the DNA sequence, since DNA sequence design problem under the constraints of Hamming distance, secondary structure and molecular thermodynamic is known to be NP-hard. For the sake of achieving the lower melting temperature and similarity for the generated DNA sequence, we proposed an improved method for the bacterial foraging algorithm based on activity of bacteria (BFA-A). In particular, the effect of bacterial vitality on foraging ability is considered, and a competitive exclusion mechanism is introduced to improve the quality of the generated DNA sequences. In BFA-A, high-quality DNA strands are replicated to avoid the participation of inferior strands in the operation, and the active regulation mechanism and the competitive rejection mechanism are used to improve and accelerate the chemotaxis process. Experiments show that our proposed approach significantly outperforms existing methods in terms of melting temperature and similarity. In addition, the experimental results also show that our method can reduce the number of iterations, and has guiding significance to generate high-quality DNA sequences more efficiency.

Keywords

• DNA computing
• DNA sequence design
• optimization methods