Boltzmann probability of RNA structural neighbors and riboswitch detection.
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.
Freyhult
Eva
E
Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden.
Moulton
Vincent
V
Clote
Peter
P
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
D016337:RNA, Catalytic