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, *
* Corresponding author
4 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
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/.
Complete list of metadatas

Cited literature [3 references]  Display  Hide  Download

https://hal.inria.fr/hal-00766780
Contributor : Yann Ponty <>
Submitted on : Wednesday, December 19, 2012 - 1:32:39 AM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM
Long-term archiving on : Wednesday, March 20, 2013 - 11:30:43 AM

Files

recomb2013twoPageAbstract.pdf
Files produced by the author(s)

Identifiers

  • HAL Id : hal-00766780, version 1

Collections

Citation

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. ⟨hal-00766780⟩

Share

Metrics

Record views

504

Files downloads

245