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 base pairs from an arbitrary initial structure of a given RNA sequence. The algorithm, which runs in quartic time and quadratic space , 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/.
Keywords for this software
References in zbMATH (referenced in 3 articles , 1 standard article )
Showing results 1 to 3 of 3.
- Clote, Peter; Bayegan, Amir H.: RNA folding kinetics using Monte Carlo and Gillespie algorithms (2018)
- Riechert, Maik; Höner zu Siederdissen, Christian; Stadler, Peter F.: Algebraic dynamic programming for multiple context-free grammars (2016)
- Senter, Evan; Sheikh, Saad; Dotu, Ivan; Ponty, Yann; Clote, Peter: Abstract: using the fast Fourier transform to accelerate the computational search for RNA conformational switches (2013) ioport
Further publications can be found at: http://bioinformatics.bc.edu/clotelab/FFTbor/index.spy?tab=references