title: Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.
abstract: BACKGROUND
  Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions.
  
  
  RESULTS
  We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models.
authors: Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK. anderson@stats.ox.ac.uk
authors: James W J
authors: JW
authors: Anderson
authors: Pierre A
authors: PA
authors: Haas
authors: Leigh-Anne
authors: LA
authors: Mathieson
authors: Vladimir
authors: V
authors: Volynkin
authors: Rune
authors: R
authors: Lyngsø
authors: Paula
authors: P
authors: Tataru
authors: Jotun
authors: J
authors: Hein
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D019143:Evolution, Molecular; D007700:Kinetics; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: D012313:RNA