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Evolutionary Algorithm for RNA Secondary Structrue Prediction Based on Simulated SHAPE Data



Welcome to the Evolutionary Algorithm for RNA Secondary Structrue Prediction Based on Simulated SHAPE Data (ESD-Fold) webserver !

ESD-Fold is a new method to predict RNA secondary structure based on both minimum free energy and SHAPE- directed pseudo-free energy. For each RNA sequence, this method employs a base pair probability matrix of all potential stems to construct a population of RNA secondary structures. It should be noted that RNAfold software, that is free of charge for academic users and available in address "http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi", is applied to compute the matrix. Then, for each constructed secondary structure, its SHAPE data is simulated. After that, an evolutionary algorithm is used to improve each structure based on both free and pseudo-free energies. Population generation is continued until the best individual in the two last populations remains fixed. Then, a structure with minimum summation of free energy and pseudo-free energy is considered as the predicted RNA secondary structure.



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