Protein Max Identity

Require proteins, or longest ORFs from DNA, to stay below a maximum identity to references.

License: This constraint can use multiple tools, each under its own license. See the Tools Used tab and each tool’s page for license details.

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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Tools Used Tools Used Source Source

proto-bio/proto-language/proto_language/constraint/protein_quality/protein_max_identity_constraint.py

View source

Require top-hit MMseqs2 identity to remain below a maximum threshold.

API Reference

ConfigProteinMaxIdentityConfig Source

Configuration for maximum identity to a protein reference set.

mmseqs_db · string · required

Path to MMseqs2 target database (FASTA file or MMseqs2 createdb output).

max_identity · number · default: "90.0"

Maximum allowed percent identity (0-100, inclusive) to the top reference hit.

pass_no_hits · boolean · default: "True"

If True, proposals with no MMseqs2 hit pass as novel sequences.

reference_fasta · string

Optional FASTA file for recovering the top hit sequence by target ID.

mmseqs_config · Mmseqs2SearchProteinsConfig

Advanced MMseqs2 protein search configuration.

ReturnsConstraintOutput

One output per proposal. A score of 0.0 passes and 1.0 fails. Metadata contains top-hit identity, target ID, target sequence when available, and selected ORF details for DNA.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import protein_max_identity_constraint, ProteinMaxIdentityConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	protein-max-identity
Function	protein_max_identity_constraint
Category	protein_quality
Mode	discrete
Uses GPU	False
Supported Types	dna, protein