ArticlePloS one2012
Using the fast fourier transform to accelerate the computational search for RNA conformational switches.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp.BMC bioinformatics · 2020Article
- RNA folding kinetics using Monte Carlo and Gillespie algorithms.Journal of mathematical biology · 2018Article
- PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.Genome biology · 2018Article
- Secondary structural entropy in RNA switch (Riboswitch) identification.BMC bioinformatics · 2015Article
- Fast, approximate kinetics of RNA folding.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- RNA folding pathways and kinetics using 2D energy landscapes.Journal of mathematical biology · 2015Article
- Complete RNA inverse folding: computational design of functional hammerhead ribozymes.Nucleic acids research · 2014Article
- Computing the probability of RNA hairpin and multiloop formation.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures.Algorithms for molecular biology : AMB · 2014Article
- Efficient calculation of exact probability distributions of integer features on RNA secondary structures.BMC genomics · 2014Article
- A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.Bioinformatics (Oxford, England) · 2013Article
- Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic.PloS oneArticle
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
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