Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars
2011
PPfold: A Fast RNA Structure Prediction Tool
Sample size: 24
publication
Evidence: high
Author Information
Author(s): Sükösd Zsuzsanna, Knudsen Bjarne, Værum Morten, Kjems Jørgen, Andersen Ebbe S
Primary Institution: Aarhus University
Hypothesis
Can a multithreaded version of the pfold algorithm improve RNA secondary structure predictions?
Conclusion
PPfold is capable of fast, high-quality predictions of large RNA secondary structures.
Supporting Evidence
- PPfold predicts the secondary structure of an alignment of 24 complete HIV-1 genomes in 65 minutes on an 8-core machine.
- PPfold has improved accuracy over the original pfold algorithm for longer RNA sequences.
- PPfold addresses floating-point underflow issues that hindered previous algorithms.
Takeaway
PPfold is a new computer program that helps scientists predict the shapes of RNA quickly and accurately, even for long RNA sequences.
Methodology
PPfold uses a multithreaded approach to distribute phylogenetic calculations and the inside-outside algorithm for RNA structure predictions.
Limitations
The algorithm's space complexity remains O(L2), requiring significant memory for long sequences.
Digital Object Identifier (DOI)
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