# Plant Genomics

This MCP server lets an agent query plant gene databases such as Ensembl Plants, UniProt, KEGG, STRING and AlphaFold, pulling together answers from several sources at once.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 8
- Author: musharna
- License: MIT · policy=link-only · description only; the file stays with the author
- Source: https://github.com/musharna/plant-genomics-mcp
- Updated: 2026-10-24
- HTML: https://affpapa.org/en/nevibecode/mcp/plant-genomics

## What it does

The server wires up 56 tools backed by 23 free public plant databases, with deeper coverage for 12 species. Tools cover gene records, sequences, protein structures, pathways, interactions, homology, TF motifs and variation; most accept a locus such as `AT1G01010` with an optional `organism=` argument, and synthesis tools like `gene_report` or the `batch_*` set merge results across sources into one answer.

Every tool is marked read-only, so the server only fetches data and never writes anything back to a project. The default stdio mode needs no setup; a separate `plant-genomics-mcp-http` binary serves streamable HTTP, and you have to host it yourself since there's no public endpoint.

The author's own benchmark on 52 questions found Claude alone declined most lookups without the server, while against plain web search the accuracy difference wasn't statistically significant.

## Requirements
- Needs: Python and uv (commands run via uvx)

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add plant-genomics-mcp -- uvx plant-genomics-mcp
```
uvx runs the command named after the package; if the README names another one, use uvx --from plant-genomics-mcp <command>

### Codex

**Platform CLI**
```bash
codex mcp add plant-genomics -- uvx plant-genomics-mcp
```
uvx runs the command named after the package; if the README names another one, use uvx --from plant-genomics-mcp <command>

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "plant-genomics": {
            "command": "uvx",
            "args": [
                "plant-genomics-mcp"
            ]
        }
    }
}
```
uvx runs the command named after the package; if the README names another one, use uvx --from plant-genomics-mcp <command>

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "plant-genomics": {
            "type": "stdio",
            "command": "uvx",
            "args": [
                "plant-genomics-mcp"
            ]
        }
    }
}
```
uvx runs the command named after the package; if the README names another one, use uvx --from plant-genomics-mcp <command>

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add plant-genomics uvx plant-genomics-mcp
```
uvx runs the command named after the package; if the README names another one, use uvx --from plant-genomics-mcp <command>

## When to use it
- look up a plant gene by locus ID
- pull a protein structure and domain data for a gene
- check orthologs of a gene across species
- gather KEGG pathways and interaction partners for a locus
- cross-check one gene across several databases in a single answer

## Example prompts
- Tell me everything about Arabidopsis gene AT1G01010 — function, GO terms, KEGG pathways and interaction partners
- Find the rice ortholog of AT1G01010 and check whether other sources confirm it
- Build a gene report for Os01g0100100 with organism=oryza_sativa

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