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Media type:
E-Article
Title:
SHAPE directed RNA folding
Contributor:
Lorenz, Ronny;
Luntzer, Dominik;
Hofacker, Ivo L.;
Stadler, Peter F.;
Wolfinger, Michael T.
imprint:
Oxford University Press (OUP), 2016
Published in:Bioinformatics
Language:
English
DOI:
10.1093/bioinformatics/btv523
ISSN:
1367-4811;
1367-4803
Origination:
Footnote:
Description:
<jats:title>Abstract</jats:title>
<jats:p>Summary: Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the ViennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure.</jats:p>
<jats:p>Availability and implementation: The capability for SHAPE directed RNA folding is part of the upcoming release of the ViennaRNA Package 2.2, for which a preliminary release is already freely available at http://www.tbi.univie.ac.at/RNA.</jats:p>
<jats:p>Contact: michael.wolfinger@univie.ac.at</jats:p>
<jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p>