Alignment Gap Gini

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.

Go to Tool Page

evo-design/proto-language/proto_language/constraint/sequence_alignment/gap_gini_constraint.py

View source

@article{katoh2013mafft,
  title={MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
  author={Katoh, Kazutaka and Standley, Daron M},
  journal={Molecular Biology and Evolution},
  volume={30},
  number={4},
  pages={772--780},
  year={2013},
  publisher={Oxford University Press},
  doi={10.1093/molbev/mst010}
}

Constraint contributorsdguo8412

Score pairwise protein alignments by gap-distribution Gini coefficient.

1. Aligns the two protein sequences with MAFFT.
2. Optionally trims (center-crop 80%, strip end gaps).
3. Computes gap run-length Gini for both sequences; takes the max.
4. Returns 0.0 if gap_gini <= max_gap_gini, else scales linearly to 1.0.

​

API Reference

​

Usage

from proto_language.core import Constraint
from proto_language.constraint import gap_gini_constraint, GapGiniConfig

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

scores = constraint.evaluate()

​

Metadata