CRISPR tracrRNA

Predict tracrRNA candidates for CRISPR loci and optionally require IntaRNA support.

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.

---

Tools Used Tools Used Source Source Cite Cite

Go to Tool Page

proto-bio/proto-language/proto_language/constraint/sequence_annotation/tracr_rna_constraint.py

View source

@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}
}

Copy citation

Require a CRISPRtracrRNA tracrRNA candidate in each DNA sequence.

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.

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.

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()

Metadata

Property	Value
Key	crispr-tracr-rna
Function	crispr_tracr_rna_constraint
Category	sequence_annotation
Mode	discrete
Uses GPU	False
Supported Types	dna