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. 2012 Jul 2:5:341.
doi: 10.1186/1756-0500-5-341.

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

M Shel Swenson  1 , Joshua Anderson, Andrew Ash, Prashant Gaurav, Zsuzsanna Sükösd, David A Bader, Stephen C Harvey, Christine E Heitsch
Affiliations

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

M Shel Swenson et al. BMC Res Notes. .

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.

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Figures

Figure 1
Figure 1
Dependencies. Figure 1 shows the dependencies in the dynamic programming algorithm. The (i,j) entry is dependent on the entries in the triangle (A,B,C).
Figure 2
Figure 2
Running time vs. sequence length. Figure 2 shows the effect of sequence length on the running time of GTfold (run using 1, 2, 4, 8, and 16 cores), RNAfold, and UNAfold.
Figure 3
Figure 3
Sensitivity vs. selectivity. Figure 3 plots selectivity against sensitivity for GTfold, RNAfold, and UNAfold on 223 16S sequences and for 55 23S sequences. The gray circles are (selectivity, sensitivity) pairs for an individual sequence, while the black dot shows the (average selectivity, average sensitivity) for a given method on a given class of sequences.
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