Polymer Genomics MCP Server

MCP server providing 70+ tools for querying the Polymer Genomics curated genomic reference database. Covers DNA biophysics, methylation probes, epigenetic clocks, gene expression/constraint, transposable elements, HLA alleles, and more — all on hg38/hg37.

Quick Start

uvx polymer-genomics-mcp

Or install permanently:

uv tool install polymer-genomics-mcp
polymer-genomics-mcp

Claude Code / Claude Desktop

Add to your MCP configuration:

{
  "mcpServers": {
    "polymer-genomics": {
      "command": "uvx",
      "args": ["polymer-genomics-mcp"]
    }
  }
}

Configuration

For local development:

{
  "mcpServers": {
    "polymer-genomics": {
      "command": "uvx",
      "args": ["polymer-genomics-mcp"],
      "env": {
        "POLYMER_API_BASE": "http://localhost:8000"
      }
    }
  }
}

What's Inside

70+ tools organized by domain:

• Gene lookup — coordinates, exons, aliases, constraint, expression, pathways
• Probe lookup — Illumina 450K/EPIC/EPICv2 with CpG context and crossmap
• Region queries — any genomic interval with layer filtering and pagination
• DNA biophysics — stacking energy, curvature, groove geometry, form propensity
• Sequence evaluation — physics linter for synthetic construct design
• Epigenetic clocks — probe sets, clock-biophysics correlation
• HLA — allele lookup, expression correlation, noncoding divergence
• Transposable elements — family lookup, methylation, platform coverage
• Cross-layer — correlate and intersect any two annotation layers

All coordinates are 1-based closed. Responses include epistemic metadata (evidence class, provenance, version).

Links

• Live database: polymerbio.org
• API docs: api.polymerbio.org/docs
• Python SDK: pip install polymer-genomics
• Source: github.com/beldez01/Polymer-Genomics-API