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Annual International Conference on Research in Computational Molecular Biology

RECOMB 2013: Research in Computational Molecular Biology pp 264–265Cite as

Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7821))

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

  1. 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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  2. Freyhult, E., Moulton, V., Clote, P.: Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics 23(16), 2054–2062 (2007)

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  3. Serganov, A., Yuan, Y.R., Pikovskaya, O., Polonskaia, A., Malinina, L., Phan, A.T., Hobartner, C., Micura, R., Breaker, R.R., Patel, D.J.: Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11(12), 1729–1741 (2004)

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Author information

Authors and Affiliations

  1. Biology Department, Boston College, Chestnut Hill, MA, 02467, USA

    Evan Senter, Ivan Dotu & Peter Clote

  2. Computer Science Department, University of Florida, Gainesville, FL, 32601, USA

    Saad Sheikh

  3. Laboratoire d’Informatique, Ecole Polytechnique, F-91128, Palaiseau Cedex, France

    Yann Ponty

Authors
  1. Evan Senter
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  2. Saad Sheikh
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  3. Ivan Dotu
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  4. Yann Ponty
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  5. Peter Clote
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Editor information

Editors and Affiliations

  1. School of Mathematics, Peking University, Beijing, P.R. China

    Minghua Deng

  2. Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, 100084, Beijing, P.R. China

    Rui Jiang

  3. Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA

    Fengzhu Sun

  4. Department of Automation, Tsinghua University, P.O. Box, 100084, Beijing, China

    Xuegong Zhang

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© 2013 Springer-Verlag Berlin Heidelberg

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Cite this paper

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

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-37194-3

  • Online ISBN: 978-3-642-37195-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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