Codon Adaptation Index

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.

Source

evo-design/proto-language

View source

Constraint contributors

Score coding-sequence proposals by Codon Adaptation Index.

API Reference

ConfigCodonAdaptationIndexConfig Source

Configuration for the Codon Adaptation Index (CAI) constraint.Exactly one reference source must be given: an explicit reference_weights table, or a reference_sequences set from which relative adaptiveness is derived.

object

Codon -> relative adaptiveness in (0,1]; provide this or reference_sequences.

array

Reference coding sequences to derive relative adaptiveness from.

enum

default:"max"

Whether to maximize (‘max’) or minimize (‘min’) the codon adaptation index.Options: max, min

number

default:"0.7"

CAI value mapped to energy 0.5 (tunable; CAI is in (0, 1]).

number

default:"0.15"

Positive float32-safe width of the sigmoid transform; larger is gentler.

ReturnsConstraintOutput

One result per sequence. score is in [0.0, 1.0] (lower is better in the requested direction); metadata carries the raw cai.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import codon_adaptation_index_constraint, CodonAdaptationIndexConfig

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

scores = constraint.evaluate()

Metadata

Property	Value
Key	`codon-adaptation-index`
Function	`codon_adaptation_index_constraint`
Category	`sequence_composition`
Mode	`discrete`
Uses GPU	`False`
Supported Types	`dna`, `rna`

Language

Language Concepts

Language Guides

Constraints

Generators

Optimizers

Codon Adaptation Index

API Reference

Usage

Metadata

​API Reference

​Usage

​Metadata

API Reference

Usage

Metadata