ViennaRNA protocols

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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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  • 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

 (3)
2017
PMCID: 5621023
PMID: 28930175
DOI: 10.3390/s17092157

[…] that would prevent the hybridization to the target amplicon, the selected capture probes were then subsequently tested with geneious 6.1.8 software (biomatters, ltd., auckland, new zealand) with the viennarna package [], implementing the microarray hybridization temperature and energy model []., previous studies have documented maximal lengths of optimal spacer sequence to be about 10–18 […]

2017
PMCID: 5621056
PMID: 28867802
DOI: 10.3390/s17091990

[…] is present in a structural context, e.g., partially structured binding site in the equilibrium ensemble, can also be obtained computationally e.g., using the constraint framework implemented in the viennarna package []. in either case one computes, in addition to the total partition function z, the constrained partition function z∗ that enforces the presence of the required structural motif. […]

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 []. the rnaplfold program of the viennarna package [] originally used the algorithm introduced in [], but has been rewritten to use the efficient version of the algorithm presented below., since our algorithm is based on mccaskill's […]


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ViennaRNA in publications

 (178)
PMCID: 5953923
PMID: 29765080
DOI: 10.1038/s41598-018-25578-3

[…] - 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., data from the mirbase set and the putative mirtrons set were used to construct the training set and the test set. in order to do so, 200 randomly chosen […]

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 […]

PMCID: 5913331
PMID: 29719549
DOI: 10.3389/fgene.2018.00124

[…] datasheet ., 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) ()., for the synteny analysis, amino acid sequences of all protein-coding genes overlapping a window 3 kb […]

PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192

[…] 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 []., in order to characterize sequenced isolates, full genome sequences were compared to a subset of full genome […]

PMCID: 5886760
PMID: 29409859
DOI: 10.1016/j.molp.2018.01.008

[…] positive reactivity of all nucleotides to obtain the normalized reactivity, θnorm(i). when we folded rnas with θnorm(i), negative reactivity was excluded according to the requirement of rnafold (viennarna-2.3.3). reactivity on guanine (g) and uracil (u) was also excluded. in genome-wide analyses, the reactivity, θfinal(i), was calculated by(equation 2)θfinal(i)=max(θnorm(i),0)., […]


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

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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.