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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).
Codex 또는 Claude로 설치 이 Prompt를 복사해 Codex, Claude 또는 다른 어시스턴트에 붙여 넣으면 Skill 페이지를 검토하고 설치를 진행할 수 있습니다.
SOC 직업 분류 기준
Predict optimal construct boundaries for protein expression. Use when the user asks about domain boundaries, construct design, truncations, which region of a protein to express, or identifying disordered regions.
Manage lab notebook entries, registry items (plasmids, proteins, etc.), templates, widgets, and audit logs via the Labbook service. Use when creating or viewing lab notebook entries, managing the sample registry, or documenting experiments.
Verify open reading frames (ORFs) in plasmid sequences. Use when the user asks about verifying protein coding sequences, checking if an ORF is present in a plasmid, finding where a protein is encoded, or doing six-frame translation analysis.
Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus.
Design PCR primers for molecular cloning. Use when the user asks about designing primers, LIC cloning primers, sequencing primers, Gibson assembly primers, or working with NCBI accession codes for cloning.
Calculate protein parameters (MW, pI, extinction coefficient) and generate purification recommendations. Use when the user asks about protein properties, molecular weight, isoelectric point, extinction coefficients, or purification strategies.
| 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). |
Use the Python CLI at scripts/codon_optimize_cli.py.
The CLI loads credentials from .env:
IDT_CLIENT_IDIDT_CLIENT_SECRETIDT_USERNAME (IDT account email)IDT_PASSWORD (IDT account password)python3 scripts/codon_optimize_cli.py --accession NP_003161 --organism insect --name SUPT6H
python3 scripts/codon_optimize_cli.py --sequence MKTLLLTLVVV... --organism ecoli --name MyProtein
python3 scripts/codon_optimize_cli.py --accession NP_003161 --vector 438-C
python3 scripts/codon_optimize_cli.py --accession NP_003161 --residues 1-500 --organism human
| 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 |
| 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 Pattern | Organism |
|---|---|
438-* | insect |
1-* | ecoli |
pVEX-* | human |
Returns optimized DNA sequence with: