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Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information.

Abstract:

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, ...

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Publication status:
Published

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Publisher copy:
10.1093/bioinformatics/btt050

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Institution:
University of Oxford
Division:
MPLS
Department:
Statistics
Role:
Author
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Institution:
University of Oxford
Division:
MPLS
Department:
Mathematical Institute
Oxford college:
Magdalen College
Role:
Author
ORCID:
0000-0002-6663-0393
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Institution:
University of British Columbia
Role:
Author
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Institution:
European Bioinformatics Institute
Role:
Author
ORCID:
0000-0001-7785-0482
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Institution:
University of Oxford
Division:
MPLS
Department:
Statistics
Role:
Author
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Biotechnology and Biological Sciences Research Council More from this funder
Publisher:
Oxford University Press (OUP) Publisher's website
Journal:
Bioinformatics Journal website
Volume:
29
Issue:
6
Pages:
704-710
Place of publication:
England
Publication date:
2013-02-08
DOI:
EISSN:
1367-4811
ISSN:
1367-4803
Pmid:
23396120
Language:
English
Keywords:
Pubs id:
384144
Local pid:
pubs:384144
Deposit date:
2020-06-05

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