MCP server for the Polymer Genomics API — curated genomic reference data via Model Context Protocol
Project description
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
| Variable | Default | Description |
|---|---|---|
POLYMER_API_BASE |
https://api.polymerbio.org |
API endpoint |
POLYMER_API_KEY |
(empty) | API key (optional) |
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
Release history Release notifications | RSS feed
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