Journal
BIOINFORMATICS
Volume 23, Issue 16, Pages 2054-2062Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btm314
Keywords
-
Ask authors/readers for more resources
Motivation: 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 <= m, in run time O ( mn(3)) and memory O( mn(2)), 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. Availability: http://bioinformatics.bc.edu/clotelab/RNAbor/ Contact: clote@bc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available