Abstract: RNA secondary structure prediction is an important research field in bioinformatics. A new method is presented to predict RNA secondary structure based on hybrid ant colony system and genetic algorithm. The relationship information between different stems is used to generate the initial population and the accumulated pheromone information is used to construct new secondary structure. Then the folding pathway is simulated, including such processes as construction of the heuristic information, the rule of initializing the pheromone, the mechanism of choosing the initial and next stem and the strategy of updating the pheromone between two different stems. And a new crossover strategy is proposed. By testing the RNA sequences with known structures, experiment result shows that this algorithm improves the prediction accuracy compared with genetic algorithm.

Key words: bioinformatics, RNA, secondary structure, ant colony system, genetic algorithm