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Open Access Technical Note

GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops

M Shel Swenson1, Joshua Anderson12, Andrew Ash12, Prashant Gaurav2, Zsuzsanna Sükösd134, David A Bader2, Stephen C Harvey5 and Christine E Heitsch1*

Author Affiliations

1 School of Mathematics, Georgia Institute of Technology, Atlanta, GA, USA

2 College of Computing, Georgia Institute of Technology, Atlanta, GA, USA

3 Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark

4 Department of Molecular Biology, Aarhus University, Aarhus, Denmark

5 School of Biology, Georgia Institute of Technology, Atlanta, GA, USA

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BMC Research Notes 2012, 5:341  doi:10.1186/1756-0500-5-341

Published: 2 July 2012

Abstract

Background

Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction programs achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage of today’s computing technology.

Findings

We present here the first implementation of RNA secondary structure prediction by thermodynamic optimization for modern multi-core computers. We show that GTfold predicts secondary structure in less time than UNAfold and RNAfold, without sacrificing accuracy, on machines with four or more cores.

Conclusions

GTfold supports advances in RNA structural biology by reducing the timescales for secondary structure prediction. The difference will be particularly valuable to researchers working with lengthy RNA sequences, such as RNA viral genomes.