Protein Nearest-Neighbor Gap Gini

Align proteins (or longest ORFs from DNA) to the nearest reference hit and score gap concentration.

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_nearest_neighbor_gap_gini_constraint.py

View source

Require low gap Gini against the nearest reference protein.

API Reference

ConfigProteinNearestNeighborGapGiniConfig Source

Configuration for gap Gini against nearest protein neighbors.

mmseqs_db · string · required

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

reference_fasta · string · required

FASTA file used to recover top-hit sequences by target ID.

max_gap_gini · number · default: "0.1"

Maximum acceptable gap Gini (0-1, inclusive) against the nearest reference protein.

pass_no_hits · boolean · default: "True"

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

trim_alignment · boolean · default: "True"

Center-crop the pairwise alignment and strip end gaps before computing gap Gini.

mmseqs_config · Mmseqs2SearchProteinsConfig

Advanced MMseqs2 protein search configuration.

mafft_config · MafftConfig

Advanced MAFFT pairwise alignment configuration.

ReturnsConstraintOutput

One output per proposal. A score of 0.0 passes and 1.0 fails. Metadata contains the nearest target ID, nearest hit sequence, and computed gap Gini.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import protein_nearest_neighbor_gap_gini_constraint, ProteinNearestNeighborGapGiniConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	protein-nearest-neighbor-gap-gini
Function	protein_nearest_neighbor_gap_gini_constraint
Category	protein_quality
Mode	discrete
Uses GPU	False
Supported Types	dna, protein