Longest ORF Length

Require a minimum-length canonical ATG-to-stop ORF on either strand.

License: ORFipy is open source and free for academic and commercial use under an MIT 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/orf_length_constraint.py

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@article{singh2021orfipy,
  title={orfipy: a fast and flexible tool for extracting ORFs},
  author={Singh, Urminder and Wurtele, Eve Syrkin},
  journal={Bioinformatics},
  volume={37},
  number={18},
  pages={3019--3020},
  year={2021},
  publisher={Oxford University Press},
  doi={10.1093/bioinformatics/btab090}
}

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Require the longest canonical ORF in each DNA sequence to meet a length threshold.

API Reference

ConfigLongestOrfLengthConfig Source

Configuration for selecting sequences by their longest canonical ORF.

min_nucleotide_length · integer · default: "3000"

Minimum nucleotide length for the longest canonical ATG-to-stop ORF.

ReturnsConstraintOutput

One output per proposal. A score of 0.0 passes and 1.0 fails. Metadata contains the selected protein sequence, selected ORF length, and ORFipy selection metadata.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import longest_orf_length_constraint, LongestOrfLengthConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	longest-orf-length
Function	longest_orf_length_constraint
Category	sequence_annotation
Mode	discrete
Uses GPU	False
Supported Types	dna