The Vienna RNA Websuite

By Andreas R. Gruber, Ronny Lorenz, Stephan H. Bernhart, Richard Neuböck, Ivo L. Hofacker. Nucleic Acids Res., 2008

2,570 citations recorded by the source corpus.

The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package. Among them, we find folding of single and aligned sequences, prediction of RNA–RNA interactions, and design of sequences with a given structure. Additionally, we provide analysis of folding landscapes using the barriers program and structural RNA alignments using LocARNA. The web server together with software packages for download is freely accessible at http://rna.tbi.univie.ac.at/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a16c9effe91811720e85b6f539bbe5ac4841ae75

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Citations in the corpus

RNAstructure: web servers for RNA secondary structure prediction and analysis (2013, methodology): “Each output page displays the RNAstructure executable and the command line used to generate the results (40).”
ViennaRNA Package 2.0 (2011, methodology): “The ViennaRNA Webserver [32] facilitates an easy to use form based web browser interface to most of the programs included in the ViennaRNA Package and additional tools.”
RBPDB: a database of RNA-binding specificities (2010, background): “Users interested in predicting structure should consider the RNAfold webserver (among others) (36).”
Transcriptome-wide mapping reveals widespread dynamic regulated pseudouridylation of ncRNA and mRNA (2014, positive): “…downstream complementary arms (Piekna-Przybylska et al., 2007), separated by a constant hairpin sequence, and folded against a 20 nt region surrounding each CBF5p-dependent site using RNAcofold (Gruber et al., 2008), with parameters and constraints described in the Extended Experimental Procedures.”
Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences (2017, positive): “Free base probabilities were also calculated using RNAfold.”
Advancing RNA 3D Structure Prediction: Exploring Hierarchical and Hybrid Approaches in CASP15 (2023, methodology): “Established models such as Vfold2D, 14 – 18 Mfold, 19 RNAFold, 20,21 and RNAstructure 22 have been applied to various 2D structure prediction tasks and have become benchmarks for machine-learning based methods in the field.”
ModeRNA: a tool for comparative modeling of RNA 3D structure (2011, background): “Locarna (49) failed to align them], and no exact sequence match in a rRNA database could be found.”