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CRISPR tracrRNA
License: CRISPRtracrRNA’s own code is licensed under MIT, 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/tracr_rna_constraint.py
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@article{mitrofanov2022crisprtracrna,
  title={CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection},
  author={Mitrofanov, Alexander and Ziemann, Marcus and Alkhnbashi, Omer S and Hess, Wolfgang R and Backofen, Rolf},
  journal={Bioinformatics},
  volume={38},
  number={Supplement\_2},
  pages={ii42--ii48},
  year={2022},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btac466}
}
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Require a CRISPRtracrRNA tracrRNA candidate in each DNA sequence.

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API Reference

ConfigCrisprTracrRNAConstraintConfig Source
Configuration for tracrRNA prediction in CRISPR loci.
​
require_intarna_interaction
boolean
default:"True"
Require an IntaRNA anti-repeat interaction for the top tracrRNA candidate.
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tracr_config
CrisprTracrRNAConfig
Advanced CRISPRtracrRNA tool configuration.
ReturnsConstraintOutput
One output per proposal. A score of 0.0 passes and 1.0 fails. Metadata contains the top tracrRNA sequence, IntaRNA interaction details, interaction energy, and all candidate calls.

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Usage

python
from proto_language.core import Constraint
from proto_language.constraint import crispr_tracr_rna_constraint, CrisprTracrRNAConstraintConfig

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

scores = constraint.evaluate()

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Metadata

PropertyValue
Keycrispr-tracr-rna
Functioncrispr_tracr_rna_constraint
Categorysequence_annotation
Modediscrete
Uses GPUFalse
Supported Typesdna