ViennaRNA statistics

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Protocols

ViennaRNA specifications

Information


Unique identifier OMICS_09351
Name ViennaRNA
Alternative name Vienna RNA
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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Versioning


No version available

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
PMCID: 3319429
PMID: 22115189
DOI: 10.1186/1748-7188-6-26

ViennaRNA citations

 (271)
call_split

Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods

2018
Sci Rep
PMCID: 5953923
PMID: 29765080
DOI: 10.1038/s41598-018-25578-3
call_split See protocol

[…] rowser - hairpin coordinates were made available in supplementary tables of Wen et al.. Hairpin secondary structures and free energies for both sets were calculated using RNAfold (version 2.3.3) from ViennaRNA Package with default options. […]

library_books

The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] eption of S1 with GCT). To select the most probable of alternative structure predictions, the constrained and unconstrained minimum free energy (MFE) was calculated using RNAeval and RNAfold from the Vienna RNA Package (version 2.3.3) respectively. The secondary structure with the smallest constrained MFE was considered the most likely one.To define the extent of gene rearrangement in acariform mi […]

library_books

Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid Responsive Genes

2018
Front Plant Sci
PMCID: 5944317
PMID: 29774043
DOI: 10.3389/fpls.2018.00589

[…] alignments were retained. For each alignment, a potential precursor sequence of 250 nt in length was excised and its secondary structure and minimum free energy were determined with RNAfold from the ViennaRNA package (v. 2.1.7; Lorenz et al., ). Mature miRNAs were predicted based on compatibility of the small RNA with the structure of its precursor. As per miRDeep-P notation, if both 5p and 3p mi […]

library_books

GLASSgo – Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence

2018
Front Genet
PMCID: 5913331
PMID: 29719549
DOI: 10.3389/fgene.2018.00124

[…] We created a docker container (v1.12.6) based on openSUSE 42.2 Leap and installed RNAlien version 1.3.7. Furthermore, we installed the following dependencies: RNAz (v2.1) (), ViennaRNA Package (v2.3.4) (), Infernal (v1.1.2) (), RNAcode (v0.3) () and LocARNA (v1.9.2) (). […]

library_books

Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot and Mouth Disease Virus in Africa

2018
Viruses
PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192

[…] h produces structure guided nucleotide alignment) implemented into MAFFT package [,,]. Based on this alignment, secondary structure prediction was calculated using RNAalifold algorithm implemented in ViennaRNA Package [,] and structures were visualized in the Forna visualization server []. […]

library_books

Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi

2018
Sci Rep
PMCID: 5882874
PMID: 29615754
DOI: 10.1038/s41598-018-23900-7

[…] te the optimal and sub-optimal secondary structures for the potential riboswitch candidates. These folding predictions obtained on the basis of energy minimization can be computed with UNAFold or the Vienna RNA package and can be compared to the reference riboswitch structure derived by comparative analysis or x-ray crystallography/NMR experiment. We chose to work with UNAFold for folding predicti […]

Citations

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

ViennaRNA review

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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.