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Bioinformatics Advance Access originally published online on June 14, 2007
Bioinformatics 2007 23(16):2054-2062; doi:10.1093/bioinformatics/btm314
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Boltzmann probability of RNA structural neighbors and riboswitch detection

Eva Freyhult 1, Vincent Moulton 2 and Peter Clote 3,*

1Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden, 2School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK and 3Department of Biology, Boston College, Chestnut Hill, MA 02467, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: We describe algorithms implemented in a new software package, RNAbor, to investigate structures in a neighborhood of an input secondary structure Formula 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 Formula of s is called a {delta}-neighbor of Formula if Formula and Formula 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 Formula. This computation is done simultaneously for all {delta} ≤ 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.

Availability: http://bioinformatics.bc.edu/clotelab/RNAbor/

Contact: clote{at}bc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on April 30, 2007; revised on April 30, 2007; accepted on June 5, 2007

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