title: Topology and prediction of RNA pseudoknots.
abstract: BACKGROUND
  Several dynamic programming algorithms for predicting RNA structures with pseudoknots have been proposed that differ dramatically from one another in the classes of structures considered.
  
  
  RESULTS
  Here, we use the natural topological classification of RNA structures in terms of irreducible components that are embeddable in the surfaces of fixed genus. We add to the conventional secondary structures four building blocks of genus one in order to construct certain structures of arbitrarily high genus. A corresponding unambiguous multiple context-free grammar provides an efficient dynamic programming approach for energy minimization, partition function and stochastic sampling. It admits a topology-dependent parametrization of pseudoknot penalties that increases the sensitivity and positive predictive value of predicted base pairs by 10-20% compared with earlier approaches. More general models based on building blocks of higher genus are also discussed.
  
  
  BACKGROUND
  The source code of gfold is freely available at http://www.combinatorics.cn/cbpc/gfold.tar.gz.
  
  
  BACKGROUND
  duck@santafe.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Mathematics, Center for Combinatorics, Key Laboratory of Pure Mathematics and Combinatorics, College of Life Science, Nankai University Tianjin 300071, PR China. duck@santafe.edu
authors.forename: Christian M
authors.initials: CM
authors.lastname: Reidys
authors.forename: Fenix W D
authors.initials: FW
authors.lastname: Huang
authors.forename: Jørgen E
authors.initials: JE
authors.lastname: Andersen
authors.forename: Robert C
authors.initials: RC
authors.lastname: Penner
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Markus E
authors.initials: ME
authors.lastname: Nebel
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000145:classification; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA