title: Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data.
abstract: BACKGROUND
  Non-coding RNAs perform a wide range of functions inside the living cells that are related to their structures. Several algorithms have been proposed to predict RNA secondary structure based on minimum free energy. Low prediction accuracy of these algorithms indicates that free energy alone is not sufficient to predict the functional secondary structure. Recently, the obtained information from the SHAPE experiment greatly improves the accuracy of RNA secondary structure prediction by adding this information to the thermodynamic free energy as pseudo-free energy.
  
  
  METHODS
  In this paper, a new method is proposed to predict RNA secondary structure based on both free energy and SHAPE pseudo-free energy. For each RNA sequence, a population of secondary structures is constructed and their SHAPE data are simulated. Then, an evolutionary algorithm is used to improve each structure based on both free and pseudo-free energies. Finally, a structure with minimum summation of free and pseudo-free energies is considered as the predicted RNA secondary structure.
  
  
  CONCLUSIONS
  Computationally simulating the SHAPE data for a given RNA sequence requires its secondary structure. Here, we overcome this limitation by employing a population of secondary structures. This helps us to simulate the SHAPE data for any RNA sequence and consequently improves the accuracy of RNA secondary structure prediction as it is confirmed by our experiments. The source code and web server of our proposed method are freely available at http://mostafa.ut.ac.ir/ESD-Fold/.
authors.affiliation: Department of Computer Science, School of Mathematics, Statistics, and Computer Science, University of Tehran, Tehran, Iran.
authors.forename: Soheila
authors.initials: S
authors.lastname: Montaseri
authors.affiliation: Department of Computer Science, School of Mathematics, Statistics, and Computer Science, University of Tehran, Tehran, Iran.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Ganjtabesh
authors.affiliation: Department of Computer Science, Faculty of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Zare-Mirakabad
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D006801:Humans; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA