Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches (extended abstract)

Evan Senter 1 Saad Sheikh 2 Ivan Dotu 1 Yann Ponty 3, 4 Peter Clote 1, *
* Auteur correspondant
4 AMIB - Algorithms and Models for Integrative Biology
CNRS - Centre National de la Recherche Scientifique : UMR8623, Polytechnique - X, Inria Saclay - Ile de France, UP11 - Université Paris-Sud - Paris 11, LRI - Laboratoire de Recherche en Informatique, LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
Abstract : 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 di er by k base pairs from an arbitrary reference structure of a given RNA sequence. The algorithm, which runs in quartic time O(n4) and quadratic space O(n2), 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/.
Type de document :
Communication dans un congrès
RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China. 2013
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Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, Peter Clote. Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches (extended abstract). RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China. 2013. 〈hal-00766780〉

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