菜单
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).
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
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: