title: Efficient calculation of exact probability distributions of integer features on RNA secondary structures.
abstract: BACKGROUND
  Although the needs for analyses of secondary structures of RNAs are increasing, prediction of the secondary structures of RNAs are not always reliable. Because an RNA may have a complicated energy landscape, comprehensive representations of the whole ensemble of the secondary structures, such as the probability distributions of various features of RNA secondary structures are required.
  
  
  RESULTS
  A general method to efficiently compute the distribution of any integer scalar/vector function on the secondary structure is proposed. We also show two concrete algorithms, for Hamming distance from a reference structure and for 5'-3' distance, which can be constructed by following our general method. These practical applications of this method show the effectiveness of the proposed method.
  
  
  CONCLUSIONS
  The proposed method provides a clear and comprehensive procedure to construct algorithms for distributions of various integer features. In addition, distributions of integer vectors, that is a combination of different integer scores, can be also described by applying our 2D expanding technique.
authors.forename: Ryota
authors.initials: R
authors.lastname: Mori
authors.forename: Michiaki
authors.initials: M
authors.lastname: Hamada
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
mesh_terms: D000465:Algorithms; D005583:Fourier Analysis; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011336:Probability; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D012313:RNA