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PLoS One. 2012;7(12):e50506. doi: 10.1371/journal.pone.0050506. Epub 2012 Dec 19.

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

Author information

1
Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America.

Abstract

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/.

PMID:
23284639
PMCID:
PMC3526635
DOI:
10.1371/journal.pone.0050506
[Indexed for MEDLINE]
Free PMC Article
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