ERD: A fast and reliable tool for RNA design including constraints

Abstract

Background: The function of an RNA in cellular processes is directly related to its structure. The free energy of RNA structure in another important key to its function as only some structures with a specific level of free energy can take part in cellular reactions. Therefore, to perform a specific function, a particular RNA structure with specific level of free energy is required. For a given RNA structure, the goal of the RNA design problem is to design an RNA sequence that folds into the given structure. To mimic the biological features of RNA sequences and structures, some sequence and energy constraints should be considered in designing RNA. Although the level of free energy is important, it is not considered in the available approaches for RNA design problem. Results: In this paper, we present a new version of our evolutionary algorithm for RNA design problem, entitled ERD, and extend it to handle some sequence and energy constraints. In the sequence constraints, one can restrict sequence positions to a fixed nucleotide or to a subset of nucleotides. As for the energy constraint, one can specify an interval for the free energy ranges of the designed sequences. We compare our algorithm with INFO-RNA, MODENA, NUPACK, and RNAiFold approaches for some artificial and natural RNA secondary structures and constraints. Conclusions: The results indicate that our algorithm outperforms the other mentioned approaches in terms of accuracy, speedup, divergency, nucleotides distribution, and similarity to the natural RNA sequences. Particularly, the designed RNA sequences in our method are much more reliable and similar to the natural counterparts. The generated sequences are more diverse and they have closer nucleotides distribution to the natural one. The ERD tool and web server are freely available at http://mostafa.ut.ac.ir/corna/erd-cons/.