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Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
Abstract : Using complex roots of unity and the Fast Fourier Transform, we design a new thermodynamics-based algorithm, FFTbor, that computes the Boltzmann probability that secondary structures differ by k base pairs from an arbitrary initial 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. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/
https://hal.inria.fr/hal-00769740
Contributor : Yann Ponty <>
Submitted on : Thursday, January 3, 2013 - 10:05:00 AM
Last modification on : Monday, December 14, 2020 - 5:00:23 PM
Contributor : Yann Ponty <>
Submitted on : Thursday, January 3, 2013 - 10:05:00 AM
Last modification on : Monday, December 14, 2020 - 5:00:23 PM
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