title: Boltzmann probability of RNA structural neighbors and riboswitch detection.
abstract: BACKGROUND
  We describe algorithms implemented in a new software package, RNAbor, to investigate structures in a neighborhood of an input secondary structure S of an RNA sequence s. The input structure could be the minimum free energy structure, the secondary structure obtained by analysis of the X-ray structure or by comparative sequence analysis, or an arbitrary intermediate structure.
  
  
  RESULTS
  A secondary structure T of s is called a delta-neighbor of S if T and S differ by exactly delta base pairs. RNAbor computes the number (N(delta)), the Boltzmann partition function (Z(delta)) and the minimum free energy (MFE(delta)) and corresponding structure over the collection of all delta-neighbors of S. This computation is done simultaneously for all delta < or = m, in run time O (mn3) and memory O(mn2), where n is the sequence length. We apply RNAbor for the detection of possible RNA conformational switches, and compare RNAbor with the switch detection method paRNAss. We also provide examples of how RNAbor can at times improve the accuracy of secondary structure prediction.
  
  
  BACKGROUND
  http://bioinformatics.bc.edu/clotelab/RNAbor/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden.
authors.forename: Eva
authors.initials: E
authors.lastname: Freyhult
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
authors.forename: Peter
authors.initials: P
authors.lastname: Clote
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000648:ultrastructure*; D017423:Sequence Analysis, RNA / Q000379:methods*; D013329:Structure-Activity Relationship
chemical_list: D016337:RNA, Catalytic