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- Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, Peter Clote
- PloS one
- 2012

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… (More)

- Evan Senter, Peter Clote
- Journal of Computational Biology
- 2015

In this article, we introduce the software suite Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure S of a given RNA sequence has base pair distance x (resp. y) from reference structure A (resp. B), Hermes computes… (More)

- Yang Ding, William Andrew Lorenz, Iván Dotú, Evan Senter, Peter Clote
- Journal of Computational Biology
- 2014

We describe four novel algorithms, RNAhairpin, RNAmloopNum, RNAmloopOrder, and RNAmloopHP, which compute the Boltzmann partition function for global structural constraints-respectively for the number of hairpins, the number of multiloops, maximum order (or depth) of multiloops, and the simultaneous number of hairpins and multiloops. Given an RNA sequence of… (More)

- Evan Senter, Ivan Dotu, Peter Clote
- Journal of mathematical biology
- 2015

RNA folding pathways play an important role in various biological processes, such as (i) the hok/sok (host-killing/suppression of killing) system in E. coli to check for sufficient plasmid copy number, (ii) the conformational switch in spliced leader (SL) RNA from Leptomonas collosoma, which controls trans splicing of a portion of the '5 exon, and (iii)… (More)

- Evan Senter, Saad Sheikh, Iván Dotú, Yann Ponty, Peter Clote
- RECOMB
- 2013

We describe the broad outline of a new thermodynamics-based algorithm, FFTbor, that uses the fast Fourier transform to perform polynomial interpolation to compute the Boltzmann probability that secondary structures differ by k base pairs from an arbitrary reference structure of a given RNA sequence. The algorithm, which runs in quartic time O(n 4) and… (More)

- C T BAHNER, D BROTHERTON, +5 authors W YEE
- Journal of medicinal chemistry
- 1965

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