> For the complete documentation index, see [llms.txt](https://docs.kernel.asimov.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.kernel.asimov.com/sequence-tools/codon-optimization.md).

# Codon Optimization

Optimize coding sequences for expression in specific host organisms.

## What is Codon Optimization?

Different organisms prefer different codons (three-nucleotide sequences) for the same amino acids. Codon optimization:

* Replaces rare codons with preferred synonymous codons
* Improves translation efficiency
* Can increase protein expression levels
* Maintains the same amino acid sequence

## Running Codon Optimization

### From the Construct Editor

1. Open a construct in the editor
2. Select a CDS (coding sequence) region
3. Click **CO** in the right sidebar
4. Configure optimization parameters
5. Click **Optimize**

### Optimization Parameters

* **Target organism**: Select the expression host
  * *E. coli*
  * *S. cerevisiae*
  * *CHO cells*
  * *HEK293*
  * And more
* **Optimization strategy**: Balance between codon usage and other factors

### Advanced Options

* **Avoid sequences**: Restriction sites, splice sites
* **GC content**: Target range
* **Repeat avoidance**: Minimize sequence repeats

## Viewing Results

After optimization:

* New sequence replaces the original CDS
* Original sequence preserved in history
* Compare before/after in sequence viewer

### Optimization Report

View details about the optimization:

* Codon Adaptation Index (CAI) before/after
* GC content change
* Modified codons list
* Removed problematic sequences

## Best Practices

### When to Optimize

* Expressing genes in heterologous hosts
* Low expression from native sequences
* Synthesizing genes *de novo*

### Considerations

* Rare codons sometimes have biological function
* Consider codon context, not just frequency
* Test multiple optimization strategies

### Quality Check

After optimization:

1. Verify amino acid sequence unchanged
2. Check for introduced restriction sites
3. Review GC content
4. Confirm problematic sequences removed

## Optimization History

Track optimization runs:

1. Click **Runs** in the sidebar
2. Find codon optimization runs
3. View parameters and results
4. Compare different optimizations

## Troubleshooting

### Optimization Fails

* Verify the region is a valid CDS
* Check that start/stop codons are present
* Ensure sequence length is divisible by 3

### Unexpected Results

* Review target organism selection
* Check advanced options for conflicts
* Try different optimization strategies

## Next Steps

* [Sequence Viewer](/sequence-tools/sequence-viewer.md) — View optimized sequences
* [Sequence Analysis](/sequence-tools/analysis.md) — Analyze sequence properties
* [Simulation](/compiler-and-simulation/simulation.md) — Predict expression