title: IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.
abstract: BACKGROUND
  Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent methods for predicting RNA secondary structures cover certain classes of pseudoknotted structures, but only a few of them achieve satisfying predictions in terms of both speed and accuracy.
  
  
  RESULTS
  We propose IPknot, a novel computational method for predicting RNA secondary structures with pseudoknots based on maximizing expected accuracy of a predicted structure. IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures and approximates a base-pairing probability distribution that considers pseudoknots, leading to the capability of modeling a wide class of pseudoknots and running quite fast. In addition, we propose a heuristic algorithm for refining base-paring probabilities to improve the prediction accuracy of IPknot. The problem of maximizing expected accuracy is solved by using integer programming with threshold cut. We also extend IPknot so that it can predict the consensus secondary structure with pseudoknots when a multiple sequence alignment is given. IPknot is validated through extensive experiments on various datasets, showing that IPknot achieves better prediction accuracy and faster running time as compared with several competitive prediction methods.
  
  
  BACKGROUND
  The program of IPknot is available at http://www.ncrna.org/software/ipknot/. IPknot is also available as a web server at http://rna.naist.jp/ipknot/.
  
  
  BACKGROUND
  satoken@k.u-tokyo.ac.jp; ykato@is.naist.jp
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan. satoken@k.u-tokyo.ac.jp
authors.forename: Kengo
authors.initials: K
authors.lastname: Sato
authors.forename: Yuki
authors.initials: Y
authors.lastname: Kato
authors.forename: Michiaki
authors.initials: M
authors.lastname: Hamada
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Akutsu
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
mesh_terms: D000465:Algorithms; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA