Multiobjective Computational RNA Design using Chemical Reaction Optimization

RNA Design Problem is an optimization problem, where a stable primary structure or nucleotide sequence is obtained from a given target RNA secondary structure and is referred as NP-hard. A multiobjective approach based on metaheuristic algorithm named Chemical Reaction Optimization (CRO) combined with a non-dominated sorting approach is used in this paper. In the multiobjective aspect considering three objective functions and a constraint between target and predicted RNA sequences, we used non-dominated sorting to minimize the objective functions of a particular RNA sequence. To improve efficiency, we designed an additional operator named Repair Function to inspect and eliminate the invalid RNA sequence from the solution space. Using 29 structures of RfamDataset, the results of our proposed method named MCROiRNA for computational RNA design problem are compared with other states of the art algorithms to demonstrate that, the performance of our proposed method is satisfactory and it gives more stable sequences with less execution time.