miRNA Specificity

License: miRanda’s own code is licensed under GPL-2.0, and it federates over bundled data sources and components, each under its own license 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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evo-design/proto-language/proto_language/constraint/sequence_annotation/mirna_specificity_constraint.py

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@article{enright2003microrna,
  title={MicroRNA targets in Drosophila},
  author={Enright, Anton J and John, Bino and Gaul, Ulrike and Tuschl, Thomas and Sander, Chris and Marks, Debora S},
  journal={Genome Biology},
  volume={5},
  number={1},
  pages={R1},
  year={2003},
  doi={10.1186/gb-2003-5-1-r1}
}

@article{hofacker1994fast,
  title={Fast Folding and Comparison of RNA Secondary Structures},
  author={Hofacker, Ivo L and Fontana, Walter and Stadler, Peter F and Bonhoeffer, L. S. and Tacker, Manfred and Schuster, Peter},
  journal={Monatshefte f{\"u}r Chemie},
  volume={125},
  number={2},
  pages={167--188},
  year={1994},
  doi={10.1007/BF00818163}
}

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Constraint contributors

Score miRNA target-site burden in target DNA/RNA sequences.

API Reference

ConfigMiRNASpecificityConfig Source

Configuration for miRNA target-site specificity scoring.

List[string]

required

miRNA query sequences to scan against each target.

array

Optional identifiers for miRNA queries.

array

Optional nonnegative per-miRNA expression weights matching the miRNA query order.

enum

default:"maximize"

Whether predicted miRNA repression should be high or low.Options: maximize, minimize

number

default:"2.0"

Aggregated repression score treated as saturating success.

number

default:"150.0"

Alignment score used to normalize each miRanda hit.

number

default:"20.0"

Absolute duplex energy used to normalize each miRanda hit.

MirandaConfig

miRanda scan configuration.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import mirna_specificity_constraint, MiRNASpecificityConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	`mirna-specificity`
Function	`mirna_specificity_constraint`
Category	`sequence_annotation`
Mode	`discrete`
Uses GPU	`False`
Supported Types	`dna`, `rna`

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miRNA Specificity

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