Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

Abstract

Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, and Peter Clote 1 Biology Department, Boston College, Chestnut Hill MA 02467 USA clote@bc.edu,ivan.dotu@bc.edu,evansenter@gmail.com 2 Computer Science Department, University of Florida, Gainesville FL 32601 USA sheikh@cise.ufl.edu 3 Laboratoire d’Informatique, Ecole Polytechnique, F-91128 Palaiseau Cedex, France, yann.ponty@lix.polytechnique.fr Abstract. We describe the broad outline of a new thermodynamicsbased algorithm, FFTbor, that uses the fast Fourier transform to perform polynomial interpolation to compute the Boltzmann probability that secondary structures differ by k base pairs from an arbitrary reference structure of a given RNA sequence. The algorithm, which runs in quartic time O(n) and quadratic space O(n), is used to determine the correlation between kinetic folding speed and the ruggedness of the energy landscape, and to predict the location of riboswitch expression platform candidates. The full paper appears in PLoS ONE (2012) 19 Dec 2012. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/. We describe the broad outline of a new thermodynamicsbased algorithm, FFTbor, that uses the fast Fourier transform to perform polynomial interpolation to compute the Boltzmann probability that secondary structures differ by k base pairs from an arbitrary reference structure of a given RNA sequence. The algorithm, which runs in quartic time O(n) and quadratic space O(n), is used to determine the correlation between kinetic folding speed and the ruggedness of the energy landscape, and to predict the location of riboswitch expression platform candidates. The full paper appears in PLoS ONE (2012) 19 Dec 2012. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/.

DOI: 10.1007/978-3-642-37195-0_22

Cite this paper

@inproceedings{Senter2013AbstractUT, title={Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches}, author={Evan Senter and Saad Sheikh and Iv{\'a}n Dot{\'u} and Yann Ponty and Peter Clote}, booktitle={RECOMB}, year={2013} }