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

Senter E, Sheikh S, Dotu I, Ponty Y, Clote P - PLoS ONE (2012)

Bottom Line: 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/.

View Article: PubMed Central - PubMed

Affiliation: 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/.

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Related in: MedlinePlus

FFTbor output for the RNA attenuator for the phenylalanyl-tRNA synthetase (pheST) operon in E. coli K-12 substr.DH10B, located adjacent to the phenylalanyl-tRNA synthetase operon leader, with GenBank accession code CP000948.1/1887748-1887820 (complement). The -axis represents base pair distance to the minimum free energy structure ; -axis represents Boltzmann probability  that a structure has base pair distance  to . (Left) Probability  that base pair distance to MFE structure is . (Center) Cumulative probability  that base pair distance to MFE structure is at most . (Right) Finite difference (Derivative)  of probability that base pair distance to MFE structure is .
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pone-0050506-g001: FFTbor output for the RNA attenuator for the phenylalanyl-tRNA synthetase (pheST) operon in E. coli K-12 substr.DH10B, located adjacent to the phenylalanyl-tRNA synthetase operon leader, with GenBank accession code CP000948.1/1887748-1887820 (complement). The -axis represents base pair distance to the minimum free energy structure ; -axis represents Boltzmann probability that a structure has base pair distance to . (Left) Probability that base pair distance to MFE structure is . (Center) Cumulative probability that base pair distance to MFE structure is at most . (Right) Finite difference (Derivative) of probability that base pair distance to MFE structure is .

Mentions: Given an RNA sequence and compatible secondary structure , let denote the sum of the Boltzmann factors of all -neighbors of ; i.e.where denotes the Turner (nearest neighbor) energy [6], [7] of , kcal/mol denotes the universal gas constant and denotes absolute temperature. Since the maximum base pair distance between a given initial structure and any other structure on RNA sequence must satisfy(3)it follows that the full partition function(4)Moreover, since , we need to compute at most the values – this observation will later prove useful. The Boltzmann probability that a secondary structure has base pair distance from the initial structure can be defined from the partition function byBy graphing the probabilities as a function of , we expect to see one or more peaks at base pair distance when there is a meta-stable (low energy) structure at base pair distance from . See Figure 1 for an illustration.


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

Senter E, Sheikh S, Dotu I, Ponty Y, Clote P - PLoS ONE (2012)

FFTbor output for the RNA attenuator for the phenylalanyl-tRNA synthetase (pheST) operon in E. coli K-12 substr.DH10B, located adjacent to the phenylalanyl-tRNA synthetase operon leader, with GenBank accession code CP000948.1/1887748-1887820 (complement). The -axis represents base pair distance to the minimum free energy structure ; -axis represents Boltzmann probability  that a structure has base pair distance  to . (Left) Probability  that base pair distance to MFE structure is . (Center) Cumulative probability  that base pair distance to MFE structure is at most . (Right) Finite difference (Derivative)  of probability that base pair distance to MFE structure is .
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3526635&req=5

pone-0050506-g001: FFTbor output for the RNA attenuator for the phenylalanyl-tRNA synthetase (pheST) operon in E. coli K-12 substr.DH10B, located adjacent to the phenylalanyl-tRNA synthetase operon leader, with GenBank accession code CP000948.1/1887748-1887820 (complement). The -axis represents base pair distance to the minimum free energy structure ; -axis represents Boltzmann probability that a structure has base pair distance to . (Left) Probability that base pair distance to MFE structure is . (Center) Cumulative probability that base pair distance to MFE structure is at most . (Right) Finite difference (Derivative) of probability that base pair distance to MFE structure is .
Mentions: Given an RNA sequence and compatible secondary structure , let denote the sum of the Boltzmann factors of all -neighbors of ; i.e.where denotes the Turner (nearest neighbor) energy [6], [7] of , kcal/mol denotes the universal gas constant and denotes absolute temperature. Since the maximum base pair distance between a given initial structure and any other structure on RNA sequence must satisfy(3)it follows that the full partition function(4)Moreover, since , we need to compute at most the values – this observation will later prove useful. The Boltzmann probability that a secondary structure has base pair distance from the initial structure can be defined from the partition function byBy graphing the probabilities as a function of , we expect to see one or more peaks at base pair distance when there is a meta-stable (low energy) structure at base pair distance from . See Figure 1 for an illustration.

Bottom Line: 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/.

View Article: PubMed Central - PubMed

Affiliation: 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/.

Show MeSH
Related in: MedlinePlus