Journal
BIOINFORMATICS
Volume 29, Issue 6, Pages 704-710Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btt050
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Funding
- Engineering and Physical Sciences Research Council
- Biotechnology and Biological Sciences Research Council
- EU grant COGANGS
- Oxford Supercomputing Centre
- BBSRC [BB/D012139/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/D012139/1] Funding Source: researchfish
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Motivation: Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions. Results: We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models. Availability: http://www.stats.ox.ac.uk/similar to anderson. Contact: anderson@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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