title: TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.
abstract: BACKGROUND
  Many RNA molecules function without being translated into proteins, and function depends on structure. Pseudoknots are motifs in RNA secondary structures that are difficult to predict but are also often functionally important.
  
  
  RESULTS
  TurboKnot is a new algorithm for predicting the secondary structure, including pseudoknotted pairs, conserved across multiple sequences. TurboKnot finds 81.6% of all known base pairs in the systems tested, and 75.6% of predicted pairs were found in the known structures. Pseudoknots are found with half or better of the false-positive rate of previous methods.
authors.affiliation: Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Seetin
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
mesh_terms: D000465:Algorithms; D009169:Mycobacterium tuberculosis / Q000737:chemistry / Q000235:genetics; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry; D022661:RNA, Untranslated / Q000737:chemistry*; D043262:Ribonuclease P / Q000737:chemistry; D017423:Sequence Analysis, RNA
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated; D043262:Ribonuclease P