codon-optimize

name	codon-optimize
description	Codon optimize protein sequences for expression using IDT's API. Use when the user asks to codon optimize genes, sequences, or accessions for a target organism (insect, E. coli, mammalian, yeast) or vector (438, 1-, pVEX).

Codon Optimization (IDT)

Use the Python CLI at scripts/codon_optimize_cli.py.

Environment

The CLI loads credentials from .env:

• IDT_CLIENT_ID
• IDT_CLIENT_SECRET
• IDT_USERNAME (IDT account email)
• IDT_PASSWORD (IDT account password)

Examples

From NCBI Accession

python3 scripts/codon_optimize_cli.py --accession NP_003161 --organism insect --name SUPT6H

From Raw Protein Sequence

python3 scripts/codon_optimize_cli.py --sequence MKTLLLTLVVV... --organism ecoli --name MyProtein

Vector Inference (Infers Organism from Vector)

python3 scripts/codon_optimize_cli.py --accession NP_003161 --vector 438-C

Truncated Construct (Residue Range)

python3 scripts/codon_optimize_cli.py --accession NP_003161 --residues 1-500 --organism human

Options

Option	Description
--sequence, -s	Protein sequence (mutually exclusive with --accession)
--accession, -a	NCBI protein accession (NP_, XP_, etc.)
--residues, -r	Residue range to extract (e.g., 1-300)
--name, -n	Gene/construct name
--organism, -o	Target organism (see mapping below)
--vector, -v	Target vector (infers organism)
--json	Output as JSON
--fasta	Output as FASTA
--output, -O	Write to file

Organism Mapping

Input	IDT Organism
insect, sf9, sf21	Spodoptera frugiperda
hi5, trichoplusia	Trichoplusia ni
ecoli, bacteria	Escherichia coli K12
human, mammalian, hek	Homo sapiens
cho	Cricetulus griseus
yeast	Saccharomyces cerevisiae
pichia	Pichia pastoris

Vector → Organism Inference

Vector Pattern	Organism
438-*	insect
1-*	ecoli
pVEX-*	human

Output

Returns optimized DNA sequence with:

• Length in bp (should be 3× input aa)
• GC content percentage
• Complexity score (if available from IDT)