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Bioinformatics Advance Access published online on June 14, 2007
Bioinformatics, 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 a,*, Vincent Moulton b and Peter Clote c,*

a Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden, eva.freyhult{at}lcb.uu.se, b School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, vincent.moulton{at}cmp.uea.ac.uk, c Department of Biology, Boston College, Chestnut Hill, MA 02467, USA, clote{at}bc.edu.

*To whom correspondence should be addressed. Dr. Peter Clote, Eva Freyhult. E-mail: clote{at}bc.edu, eva.freyhult{at}lcb.uu.se


  Abstract

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 {tau} of s is called a {delta}-neighbor of S if {tau} 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(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/.

Associate Editor: Prof. Anna Tramontano

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

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