Using the fast Fourier transform to accelerate the computational search for RNA conformational switches. 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/.

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Senter, Evan; Sheikh, Saad; Dotu, Ivan; Ponty, Yann; Clote, Peter: Abstract: using the fast Fourier transform to accelerate the computational search for RNA conformational switches (2013) ioport