CRISPR Array

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.

Tools Used Tools Used Source Source Cite Cite

Go to Tool Page

evo-design/proto-language/proto_language/constraint/sequence_annotation/crispr_array_constraint.py

View source

@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}
}

Copy citation

Constraint contributors

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

API Reference

ConfigCrisprArrayConfig Source

Configuration for CRISPR array detection.

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`

Language

Language Concepts

Language Guides

Constraints

Generators

Optimizers

CRISPR Array

API Reference

Usage

Metadata

​API Reference

​Usage

​Metadata

API Reference

Usage

Metadata