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 [Formula: see text] base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm,...

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Autores principales:	Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, Peter Clote
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2e7cf30e770a41ba88b630c8ce791991
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spelling	oai:doaj.org-article:2e7cf30e770a41ba88b630c8ce7919912021-11-18T08:04:35ZUsing the fast fourier transform to accelerate the computational search for RNA conformational switches.1932-620310.1371/journal.pone.0050506https://doaj.org/article/2e7cf30e770a41ba88b630c8ce7919912012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284639/?tool=EBIhttps://doaj.org/toc/1932-6203Using 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 [Formula: see text] base pairs from an arbitrary initial 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. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/.Evan SenterSaad SheikhIvan DotuYann PontyPeter ClotePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e50506 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Evan Senter Saad Sheikh Ivan Dotu Yann Ponty Peter Clote Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
description	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 [Formula: see text] base pairs from an arbitrary initial 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. A web server is available at http://bioinformatics.bc.edu/clotelab/FFTbor/.
format	article
author	Evan Senter Saad Sheikh Ivan Dotu Yann Ponty Peter Clote
author_facet	Evan Senter Saad Sheikh Ivan Dotu Yann Ponty Peter Clote
author_sort	Evan Senter
title	Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
title_short	Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
title_full	Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
title_fullStr	Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
title_full_unstemmed	Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
title_sort	using the fast fourier transform to accelerate the computational search for rna conformational switches.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/2e7cf30e770a41ba88b630c8ce791991
work_keys_str_mv	AT evansenter usingthefastfouriertransformtoacceleratethecomputationalsearchforrnaconformationalswitches AT saadsheikh usingthefastfouriertransformtoacceleratethecomputationalsearchforrnaconformationalswitches AT ivandotu usingthefastfouriertransformtoacceleratethecomputationalsearchforrnaconformationalswitches AT yannponty usingthefastfouriertransformtoacceleratethecomputationalsearchforrnaconformationalswitches AT peterclote usingthefastfouriertransformtoacceleratethecomputationalsearchforrnaconformationalswitches
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Using the fast fourier transform to accelerate the computational search for RNA conformational switches.

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