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 differ by k base pairs from an arbitrary reference 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. The full paper appears in PLoS ONE (2012) 19 Dec 2012. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/ .
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References
Clote, P., Lou, F., Lorenz, W.A.: Maximum expected accuracy structural neighbors of an RNA secondary structure. BMC Bioinformatics 13(suppl. 5), S6 (2012)
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Senter, E., Sheikh, S., Dotu, I., Ponty, Y., Clote, P. (2013). Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science(), vol 7821. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37195-0_22
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DOI: https://doi.org/10.1007/978-3-642-37195-0_22
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