RNA Structural Motif Similarity

Compare RNA structural motifs (stems, hairpins, bulges) using Jaccard similarity.

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

This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.

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proto-bio/proto-language/proto_language/constraint/rna_secondary_structure/structure_similarity_constraint.py

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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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Compare structural motifs (stems, hairpins, bulges) between proposals and.

reference using Jaccard similarity.

Returns 1 - similarity (so 0 is perfect match, 1 is worst).

API Reference

ConfigRNAMotifSimilarityConfig Source

Configuration for structural motif similarity constraint.

Compares extracted structural motifs (stems, hairpins, bulges, nesting depth, unpaired regions) using Jaccard similarity.

Inherits from RNAStructureConstraintBaseConfig.

reference_sequence · string · required

Reference RNA/DNA sequence to compare against

temperature · number · default: "37.0"

Folding temperature in Celsius

ReturnsConstraintOutput

Per-proposal score (1 - similarity) with metadata for reference, candidate, and shared motif sets plus the predicted structure.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import rna_motif_similarity_constraint, RNAMotifSimilarityConfig

constraint = Constraint(
    inputs=[segment],
    function=rna_motif_similarity_constraint,
    function_config=RNAMotifSimilarityConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()

Metadata

Property	Value
Key	rna-motif-similarity
Function	rna_motif_similarity_constraint
Category	rna_secondary_structure
Mode	discrete
Uses GPU	False
Supported Types	dna, rna