ViennaRNA

First released in 1994, ViennaRNA is a thermodynamic RNA secondary-structure prediction package. From an RNA or DNA sequence it computes the minimum-free-energy secondary structure and its free energy using a nearest-neighbor energy model, with no training and no GPU required. It is widely used to predict and compare the base-pairing of messenger RNAs, non-coding RNAs, riboswitches, and designed RNA constructs.

TBI Vienna

License: ViennaRNA is licensed under Custom (ViennaRNA Package License) and may require explicit attribution when utilized. Please refer to the license for full terms.

Proto is not affiliated with TBI Vienna. This toolkit is open source and builds on the implementation produced by this organization. Product names, logos, and trademarks are the property of their respective owners.

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ViennaRNA/ViennaRNA

The ViennaRNA Package

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ViennaRNA Package 2.0

Ronny Lorenz, Stephan H Bernhart, … Ivo L Hofacker

Algorithms for Molecular Biology (2011)

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@article{lorenz2011viennarna,
  title={ViennaRNA Package 2.0},
  author={Lorenz, Ronny and Bernhart, Stephan H and H{\"o}ner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F and Hofacker, Ivo L},
  journal={Algorithms for Molecular Biology},
  volume={6},
  number={1},
  pages={26},
  year={2011},
  publisher={BioMed Central},
  doi={10.1186/1748-7188-6-26}
}

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proto-bio/proto-tools/proto_tools/tools/structure_prediction/viennarna

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Function	Description
run_viennarna()	RNA secondary structure prediction using ViennaRNA MFE folding	Docs Source

Background

ViennaRNA (Lorenz et al., 2011) predicts the secondary structure of a nucleic-acid sequence: the set of intramolecular base pairs that form within a single strand. Secondary structure sits between sequence and three-dimensional shape and governs how many functional RNAs behave, so predicting it from sequence alone is a core step in RNA analysis and design.

Internally, ViennaRNA folds each sequence with the minimum-free-energy dynamic program at the core of RNAfold (cubic in the sequence length) under a nearest-neighbor thermodynamic model. RNA sequences use the Turner 2004 parameters. Selecting the DNA option instead loads the Mathews 2004 DNA parameters. The predicted structure is returned in dot-bracket notation together with its minimum free energy in kcal/mol, where a more negative value indicates a more stable predicted fold. Because it is a thermodynamic rather than a learned method, it is deterministic, runs on CPU, and predicts secondary structure only, not three-dimensional coordinates.

The reference implementation is the ViennaRNA Package, maintained by TBI Vienna at ViennaRNA/ViennaRNA.

Learning Resources

• ViennaRNA Package documentation and tutorials (TBI Vienna) - the official documentation, worked tutorials, and the RNAfold web server for trying predictions interactively.

Tools

ViennaRNA Secondary Structure Prediction (viennarna-prediction)

Folds each input sequence to its minimum-free-energy secondary structure, returning the structure in dot-bracket notation and the minimum free energy in kcal/mol for every sequence.

API Reference

Source

Input: ViennaRNAInput

sequences · List[string] · required

List of RNA sequences to fold. Each sequence should contain only valid RNA nucleotides (A, U, G, C) or DNA nucleotides (A, T, G, C) which will be automatically converted to RNA (T -> U). Lowercase letters are also accepted.

Source

Config: ViennaRNAConfig

temperature · number · default: "37.0"

Temperature in Celsius for energy calculations. Affects the thermodynamic parameters used in folding. Default: 37.0 (physiological temperature).

use_dna_params · boolean · default: "False"

Whether to use DNA energy parameters instead of RNA parameters. When True, loads DNA_Mathews2004 parameters.

no_lonely_pairs · boolean · default: "False"

Disallow lonely base pairs (helices of length 1). This can reduce artifacts in structure prediction. Default: False.

dangles · enum · default: "2"

Dangling-end treatment.

Available options: 0, 1, 2, 3

circ · boolean · default: "False"

Treat as circular RNA. Default False.

max_bp_span · integer · default: "-1"

Max base-pair span; positive values forbid long-range pairing.

verbose · integer · default: "0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

device · string · default: "cpu"

Device to run the tool on.

timeout · integer · default: "600"

Maximum execution time in seconds. None waits indefinitely.

seed · integer

Random seed. When set, tools run reproducibly up to small GPU float noise (see BaseToolOutput.approx_equal), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source

Output: ViennaRNAOutput

results · List[ViennaRNAResult] · required

List of fold results, one per input sequence. Each result contains the sequence, predicted structure in dot-bracket notation, and the minimum free energy.

Show ViennaRNAResult

sequence · string · required

The input RNA sequence.

structure · string

Predicted secondary structure in dot-bracket notation.

mfe · number

Minimum free energy in kcal/mol.

Applications

Use this to predict the base-pairing of mRNAs, non-coding RNAs, riboswitches, aptamers, or designed RNA constructs from sequence alone, for example to check whether a designed UTR or guide RNA folds as intended, or to rank candidate sequences by the stability of their predicted fold.

Usage Tips

• temperature (default 37.0, degrees Celsius) sets the folding temperature. The energy model is temperature-dependent, so the predicted structure and free energy change with it. Keep the default for physiological predictions and change it to model other conditions.
• use_dna_params (default False) also changes how the input is read. When False, any T in a sequence is converted to U and the sequence is folded as RNA with the Turner 2004 parameters. Set it True to fold the sequence as DNA with the Mathews 2004 DNA parameters and no T-to-U conversion.
• Set circ to True for circular molecules. Plasmids, viroids, and circular RNAs fold differently from linear strands, and the default treats the sequence as linear.
• no_lonely_pairs (default False) forbids isolated base pairs. Enabling it removes length-one helices, which often yields more physically realistic structures.
• max_bp_span (default -1, unlimited) caps the base-pair span. Set a positive value to forbid long-range pairs, which is useful for very long sequences or local-structure analysis.

Toolkit Notes

These apply to every ViennaRNA tool in this toolkit (viennarna-prediction).

• Runs on CPU. ViennaRNA is a fast C package and does not use a GPU. Folding is near-instant for typical sequences, and runtime grows as the cube of sequence length, so very long inputs are slower.
• Predicts secondary structure only. The output is a base-pairing pattern and a free energy, not three-dimensional atomic coordinates; use a tertiary-structure method when 3D is needed.

Example notebook: See the full working example for a copy-paste-ready walkthrough.

Infrastructure Guides

The following guides cover how to run tools efficiently and at scale.

Tool Persistence

Keep a tool’s model warm across calls instead of reloading it every invocation.

Device Management

How GPUs are allocated to tools and how to target specific devices.

Parallel Execution

Fan a batch of inputs out across multiple GPUs.

Cloud Inference

Run tools on managed cloud infrastructure with no local setup.