Simulating the Folding Pathway of RNA Secondary Structure Using the Modified Ant Colony Algorithm

A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithm is proposed. For a given RNA sequence, the set of all possible stems is obtained and the energy of each stem is calculated and stored at the initial stage. Furthermore, a more realistic formula is used to compute the energy of multi-branch loop in the following iteration. Then a 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. Finally by testing RNA sequences with known secondary structures from the public databases, we analyze the experimental data to select appropriate values for parameters. The measure indexes show that our procedure is more consistent with phylogenetically proven structures than software RNAstructure sometimes and more effective than the standard Genetic Algorithm.