| 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_IDIDT_CLIENT_SECRETIDT_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)
