Fast, approximate kinetics of RNA folding

TL;DR

Hermes is a software suite that offers rapid, accurate algorithms for modeling RNA secondary structure folding kinetics, enabling analysis of large sequences for synthetic biology applications.

Contribution

The paper introduces Hermes, a novel software that uses Fourier transforms and spectral methods to efficiently compute RNA folding kinetics for large sequences.

Findings

Hermes accurately predicts RNA refolding times.

Hermes outperforms existing methods in speed and scalability.

The software is suitable for RNA design in synthetic biology.

Abstract

In this paper, 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 the exact kinetics of folding from A to B in this coarse-grained model. In particular, Hermes computes the mean first passage time from the transition probability matrix by using matrix inversion, and also computes the equilibrium time from the rate matrix by using spectral decomposition. Due to the model granularity and the speed of Hermes, it is capable of determining secondary structure refolding kinetics for large RNA sequences, beyond the range of other methods. Comparative benchmarking of Hermes with other methods indicates that Hermes provides refolding kinetics of accuracy suitable for use in computational design of RNA, an important area of synthetic biology. Source code and documentation for Hermes are available at http://bioinformatics. bc.edu/clotelab/Hermes/.