Abstract: Using the fast Fourier transform to accelerate the computational search for RNA conformational switches

Evan Senter; Saad Sheikh; Ivan Dotu; Yann Ponty; Peter Clote

doi:10.1007/978-3-642-37195-0_22

Abstract: Using the fast Fourier transform to accelerate the computational search for RNA conformational switches

Evan Senter
, Saad Sheikh
, Ivan Dotu
, Yann Ponty
, Peter Clote

Boston College
University of Florida

Résultats de recherche: Le chapitre dans un livre, un rapport, une anthologie ou une collection › Contribution à une conférence › Revue par des pairs

Résumé

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(n⁴) and quadratic space O(n²), 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/.

langue originale	Anglais
titre	Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings
Pages	264-265
Nombre de pages	2
Les DOIs	https://doi.org/10.1007/978-3-642-37195-0_22
état	Publié - 3 avr. 2013
Evénement	17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013 - Beijing, Chine Durée: 7 avr. 2013 → 10 avr. 2013

Série de publications

Nom	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	7821 LNBI
ISSN (imprimé)	0302-9743
ISSN (Electronique)	1611-3349

Une conférence

Une conférence	17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013
Pays/Territoire	Chine
La ville	Beijing
période	7/04/13 → 10/04/13

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10.1007/978-3-642-37195-0_22

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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. Dans Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings (p. 264-265). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol 7821 LNBI). https://doi.org/10.1007/978-3-642-37195-0_22

Senter, Evan ; Sheikh, Saad ; Dotu, Ivan et al. / Abstract : Using the fast Fourier transform to accelerate the computational search for RNA conformational switches. Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. 2013. p. 264-265 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

@inproceedings{dd328c46e6cc41c19d99c8cb6ca777ba,

title = "Abstract: Using the fast Fourier transform to accelerate the computational search for RNA conformational switches",

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(n4) and quadratic space O(n2), 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/.",

keywords = "Lagrange interpolation, RNA secondary structure, fast Fourier transform, partition function",

author = "Evan Senter and Saad Sheikh and Ivan Dotu and Yann Ponty and Peter Clote",

year = "2013",

month = apr,

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doi = "10.1007/978-3-642-37195-0\_22",

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series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

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booktitle = "Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings",

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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. Dans Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), VOL. 7821 LNBI, p. 264-265, 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, Beijing, Chine, 7/04/13. https://doi.org/10.1007/978-3-642-37195-0_22

Abstract: Using the fast Fourier transform to accelerate the computational search for RNA conformational switches. / Senter, Evan; Sheikh, Saad; Dotu, Ivan et al.
Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. 2013. p. 264-265 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol 7821 LNBI).

Résultats de recherche: Le chapitre dans un livre, un rapport, une anthologie ou une collection › Contribution à une conférence › Revue par des pairs

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AU - Senter, Evan

AU - Sheikh, Saad

AU - Dotu, Ivan

AU - Ponty, Yann

AU - Clote, Peter

PY - 2013/4/3

Y1 - 2013/4/3

N2 - 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(n4) and quadratic space O(n2), 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/.

AB - 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(n4) and quadratic space O(n2), 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/.

KW - Lagrange interpolation

KW - RNA secondary structure

KW - fast Fourier transform

KW - partition function

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DO - 10.1007/978-3-642-37195-0_22

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SN - 9783642371943

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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BT - Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings

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Senter E, Sheikh S, Dotu I, Ponty Y, Clote P. Abstract: Using the fast Fourier transform to accelerate the computational search for RNA conformational switches. Dans Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings. 2013. p. 264-265. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-37195-0_22

Abstract: Using the fast Fourier transform to accelerate the computational search for RNA conformational switches

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