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

PLOS ONE, 2012, vol. 7, issue 12, 1-13

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 base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm, which runs in quartic time and quadratic space , 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/.

Date: 2012
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0050506

DOI: 10.1371/journal.pone.0050506

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