title: RnaPredict--an evolutionary algorithm for RNA secondary structure prediction.
abstract: This paper presents two in-depth studies on RnaPredict, an evolutionary algorithm for RNA secondary structure prediction. The first study is an analysis of the performance of two thermodynamic models, Individual Nearest Neighbor (INN) and Individual Nearest Neighbor Hydrogen Bond (INN-HB). The correlation between the free energy of predicted structures and the sensitivity is analyzed for 19 RNA sequences. Although some variance is shown, there is a clear trend between a lower free energy and an increase in true positive base pairs. With increasing sequence length, this correlation generally decreases. In the second experiment, the accuracy of the predicted structures for these 19 sequences are compared against the accuracy of the structures generated by the mfold dynamic programming algorithm (DPA) and also to known structures. RnaPredict is shown to outperform the minimum free energy structures produced by mfold and has comparable performance when compared to sub-optimal structures produced by mfold.
authors.forename: Kay
authors.initials: K
authors.lastname: Wiese
authors.forename: Alain
authors.initials: A
authors.lastname: Deschenes
authors.forename: Andrew
authors.initials: A
authors.lastname: Hendriks
mesh_terms: D000465:Algorithms; D000818:Animals; D020029:Base Pairing; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
chemical_list: D012313:RNA