A Novel Genetic Algorithm for Nucleic Acid Secondary Structure Prediction with Planar Pseudoknots

作者：Zhang Kai^*; Huang Xinquan; Hu Wei; Liu Jun

来源：Journal of Computational and Theoretical Nanoscience, 2015, 12(7): 1228-1233.

DOI：10.1166/jctn.2015.3877

• Secondary Structure Prediction
• Genetic Algorithm
• Minimum Free Energy
• Dynamic Programming
• Pseudoknots

In recent years, DNA and RNA molecules have shown great potential as a design medium for the construction of nanostructures and the programmed assembly of molecular computing. In these fields, it is very significant to predict nucleic acid secondary structure. However, traditional methods could not predict the pseudoknots structure effectively. In this paper, we propose a novel genetic algorithm to predict nucleic acid secondary structure with planar pseudoknots. In our algorithm, the free energy and the number of continues base pairs stacking are used as fitness function to evaluate the individuals. A novel crossover and mutation operators are also designed to generate new children individuals efficiently. Finally, in order to validate our proposal, we have compared the results obtained by our algorithm with RNAStructure. As will be discussed, our algorithm can efficiently predict the planar pseudoknots with lower free energy and more continues base pairs stacking.

• 出版日期2015-7
• 单位武汉科技大学