ViennaRNA protocols

ViennaRNA specifications

Information


Unique identifier OMICS_09351
Name ViennaRNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C
Parallelization OpenMP
Computer skills Advanced
Version 2.4.6
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ViennaRNA_Package

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Maintainer


  • person_outline Rinverse <>

Publications for ViennaRNA

library_books

SHAPE directed RNA folding.

2016 Bioinformatics
PMCID: 4681990
PMID: 26353838
DOI: 10.1093/bioinformatics/btv523
library_books

ViennaRNA Package 2.0.

2011 Algo Mol Biol
PMCID: 3319429
PMID: 22115189
DOI: 10.1186/1748-7188-6-26

ViennaRNA IN pipelines

 (2)
2011
PMCID: 3063221
PMID: 21388531
DOI: 10.1186/1748-7188-6-3

[…] are accessible, this is no way around sampling the structures of the molecules., the first predecessor of our algorithm, not yet fully (n3), has been used in rnaup [5]. the rnaplfold program of the viennarna package [12] originally used the algorithm introduced in [10], but has been rewritten to use the efficient version of the algorithm presented below., since our algorithm is based […]

2011
PMCID: 3063221
PMID: 21388531
DOI: 10.1186/1748-7188-6-3

[…] presented below., since our algorithm is based on mccaskill's dynamic programming (dp) algorithm for the partition function [13], we briefly recapitulate the algorithm as implemented in the viennarna package. as usual, we consider only (pseudo)knot-free secondary structures and use the turner nearest-neighbor energy model [14]. in the inside (forward) recursion, the partition function […]

ViennaRNA institution(s)
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria

ViennaRNA review

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garantjm

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Desktop
ViennaRNA package is the most complete set of tools available to predict the secondary structure of RNA molecules. They're both easy to use in their default form and provide tons of options form specific use and further characterization. It is actively developed by a competent team.