bio-codon-usage
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.
npx skills add BioTender-max/awesome-bio-agent-skills --skill codon-usage --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Codon Usage Analyze codon usage patterns and calculate codon adaptation metrics using Biopython. **"Analyze codon usage"** → Count codons in a coding sequence, compute frequencies and bias metrics. - Python: `Counter` on 3-mers + `CodonAdaptationIndex` (BioPython) **"Optimize codons for expression"** → Replace codons with host-preferred synonymous codons using a preference table. - Python: custom mapping dict + `Seq()` (BioPython) ## Required Imports ```python from Bio.Seq import Seq from Bio.SeqUtils import GC123 from Bio.SeqUtils.CodonUsage import CodonAdaptationIndex from Bio.Data import CodonTable from collections import Counter ``` ## Basic Codon Counting **Goal:** Tabulate codon frequencies in a coding sequence. **Approach:** Split the sequence into triplets from the reading frame start,
- Version Compatibility
- Required Imports
- Basic Codon Counting
- Count Codons in Sequence
- Codon Frequencies (Relative)
- Codon Adaptation Index (CAI)
- Using CodonUsage Module
- CAI with Custom Codon Index
- Synonymous Codon Usage
- RSCU (Relative Synonymous Codon Usage)
- Identify Rare Codons
- Codon Bias by Position (GC123)
- Codon Tables
- Access Codon Tables
What does the bio-codon-usage skill do?
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill codon-usage --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.