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codon-optimization

Optimize DNA sequences for codon usage in a target host.

1|Updated Apr 29, 2026
Search Tags:#bioinformatics#protein#codon-optimization#dna#biotechnology#codon-harmonization#reverse-translation
One-click install
npx skills add https://github.com/cultivarium/hermes-starter-kit --skill codon-optimization
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: codon-optimization
Source: https://github.com/cultivarium/hermes-starter-kit/tree/main/skills/codon-optimization
Command: npx skills add https://github.com/cultivarium/hermes-starter-kit --skill codon-optimization

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill enables researchers to optimize coding sequences for expression in a host by recoding DNA to preferred codons, increasing protein yield and compatibility with host translation.

Core Features & Use Cases

  • Codon optimization to maximize CAI for a target organism or to match a provided codon usage table.
  • Codon harmonization to preserve translational pausing patterns and improve folding for complex proteins.
  • Reverse translation from protein sequences to DNA using a chosen codon usage profile.
  • Generate codon usage tables from GenBank or FASTA genomes and perform end-to-end workflows.

Quick Start

Provide a DNA sequence and a target organism or codon usage table to start optimizing.

Frequently Asked Questions about codon-optimization

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I codon-optimize a DNA sequence for a specific host organism?▼

To codon-optimize DNA, provide your target host organism by name or TaxID along with the DNA sequence. The Skill recodes the sequence to match preferred codon usage, maximizing the CAI for that target organism to increase protein yield.

What is the difference between codon optimization and codon harmonization?▼

Codon optimization maximizes CAI by replacing codons with the most preferred ones, while codon harmonization preserves translational pausing patterns. Harmonization maintains natural translation speeds to improve folding for complex proteins.

Can I reverse translate a protein sequence to DNA using a custom codon usage table?▼

Yes, you can reverse translate protein sequences back to DNA. Provide the protein sequence and either a target organism or a custom codon usage table in JSON or CSV format to drive the reverse translation.

How do I generate a codon usage table from a GenBank or FASTA genome file?▼

To generate a codon usage table, provide a genome file in GenBank or FASTA format as input. The Skill analyzes the genome sequence and outputs a codon usage table that can then be used for downstream optimization tasks.

Do I need a pre-built codon usage table or can I just provide a target organism name?▼

You do not need a pre-built table. You can drive the computation by providing either a target organism name or TaxID, or alternatively supply your own codon usage table in JSON or CSV format.

When should I use codon harmonization instead of full codon optimization for protein expression?▼

Use codon harmonization instead of optimization when expressing complex proteins that require proper folding. Harmonization preserves translational pausing patterns, whereas full optimization maximizes CAI which can disrupt co-translational folding.

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