CRISPR Array

Detect CRISPR repeat-spacer arrays in DNA sequences using MinCED.

License: MinCED has a GPL-3.0 license. 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/sequence_annotation/crispr_array_constraint.py

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@software{skennerton2019minced,
  title={MinCED: Mining CRISPRs in Environmental Datasets},
  author={Skennerton, Connor T and Angly, Florent},
  year={2019},
  url={https://github.com/ctSkennerton/minced},
  note={Derived from the CRISPR Recognition Tool (CRT) by Bland et al., 2007}
}

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Require a MinCED-detected CRISPR array in each DNA sequence.

API Reference

ConfigCrisprArrayConfig Source

Configuration for CRISPR array detection.

minced_config · MincedConfig

MinCED CRISPR detection configuration. Tune min_num_repeats and min_repeat_length here.

ReturnsConstraintOutput

One output per proposal. A score of 0.0 passes and 1.0 fails. Metadata contains array count, first repeat sequence, and a JSON file reference with all MinCED array calls.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import crispr_array_constraint, CrisprArrayConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	crispr-array
Function	crispr_array_constraint
Category	sequence_annotation
Mode	discrete
Uses GPU	False
Supported Types	dna