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Published in:
2013 | OriginalPaper | Chapter
Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
Authors : Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, Peter Clote
Published in: Research in Computational Molecular Biology
Publisher: Springer Berlin Heidelberg
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We describe the broad outline of a new thermodynamics-based 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
4
) and quadratic space
O
(
n
2
), 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/
.