Ensembl vs Genomics MCP

In-depth architectural comparison of the Ensembl and Genomics MCP MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

Which MCP Server Should You Choose?

Choose Ensembl when:

• You need dedicated capabilities in the Biology & Bioinformatics domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).

Explore Ensembl Details

G

Choose Genomics MCP when:

• You need dedicated capabilities in the Biology & Bioinformatics domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).

Explore Genomics MCP Details

Feature & Specification Comparison

Specification	Ensembl Biology & Bioinformatics	G Genomics MCP Biology & Bioinformatics
Summary	Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation	Bounded genomic data from archives and indexed files, with versioned reference evidence.
Category & Scope	Biology & Bioinformatics	Biology & Bioinformatics
Quality signal

Tools & Capabilities Breakdown

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-ensembl"
      ]
    }
  }
}

{
  "mcpServers": {
    "genomics-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "genomics-mcp"
      ]
    }
  }
}

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