Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
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
Show MeSH
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/. Related in: MedlinePlus |
Related In:
Results -
Collection
getmorefigures.php?uid=PMC3526635&req=5
Mentions: The output of FFTbor, as shown in Figure 2, is a probability distribution, where the -axis represents the base pair distance from an arbitrary, but fixed secondary structure , and the -axis represents the Boltzmann probability that a secondary structure has base pair distance from . Arguably, this probability distribution is an accurate one-dimensional projection of the rugged, high dimensional energy landscape near structure , of the sort artistically rendered in the well-known energy landscape depicted in Figure 1 of [12]. In the sequel, we may call the FFTbor probability distribution a structural neighbor profile, or simply structural profile. A hypothesis behind theoretical work in biomolecular folding theory in [13] is that kinetic folding slows down as the energy landscape becomes more rugged. This is borne out in our computational experiments for RNA using FFTbor, as reported in Figure 2. |
View Article: PubMed Central - PubMed
Affiliation: Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America.