How does the optimization process work?

The server uses codon usage bias data to select synonymous codons that maximize the Codon Adaptation Index (CAI) for your chosen host.

Can I avoid specific restriction sites?

Yes, when using `optimize_sequence`, you can set the avoidRestrictionSites parameter to true to minimize common enzyme recognition sites.

What hosts are supported?

The server supports a wide range of hosts including E. coli, S. cerevisiae, and H. sapiens.

Codon Usage Optimization MCP Connector for Claude

A+

Optimize DNA sequences for heterologous expression in specific hosts.

4 tools Official Updated Oct 1, 2026 Official Vinkius Partner

More Details Connect to Claude

This MCP server provides specialized tools for genetic engineering and synthetic biology. It allows users to transform protein sequences into optimized DNA sequences tailored for specific expression hosts like E. coli or H. sapiens. Use optimize_sequence to generate DNA with high CAI, analyze_codon_usage to profile sequence bias, calculate_complexity_metrics for structural analysis, and validate_host_compatibility to predict translation success.

dnacodon-optimizationbiotechnologygenomicsprotein-expression

Connect to Claude

Subscribe on Vinkius, then add this connector to Claude.ai or Claude Code.

① Claude.ai (web app)

Go to Settings → Connectors → Add custom connector
Paste the MCP endpoint URL below

https://edge.vinkius.com/vk_preview_EwhIYVMAwkqiTjDiRdWlLHasxz10yWoao2pKz7gf/mcp

② Claude Code (terminal)

claude mcp add --transport http codon-usage-optimization https://edge.vinkius.com/vk_preview_EwhIYVMAwkqiTjDiRdWlLHasxz10yWoao2pKz7gf/mcp

③ Claude Desktop

Add to claude_desktop_config.json:

{
  "mcpServers": {
    "codon-usage-optimization": {
      "url": "https://edge.vinkius.com/vk_preview_EwhIYVMAwkqiTjDiRdWlLHasxz10yWoao2pKz7gf/mcp"
    }
  }
}

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