Plant Genomics — Claude Code MCP server: what it does, how to install
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.
claude mcp add plant-genomics-mcp -- uvx plant-genomics-mcpWhat Plant Genomics 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.
What it helps with
- 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 for the agent
- 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
How to install Plant Genomics
Platform CLI
claude mcp add plant-genomics-mcp -- uvx plant-genomics-mcpuvx runs the command named after the package; if the README names another one, use uvx --from plant-genomics-mcp <command>
Platform CLI
codex mcp add plant-genomics -- uvx plant-genomics-mcpuvx runs the command named after the package; if the README names another one, use uvx --from plant-genomics-mcp <command>
Config file
{
"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>
Config file
{
"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>
Platform CLI
gemini mcp add plant-genomics uvx plant-genomics-mcpuvx runs the command named after the package; if the README names another one, use uvx --from plant-genomics-mcp <command>
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about Plant Genomics
How do I install Plant Genomics in Claude Code?
Run claude mcp add plant-genomics-mcp -- uvx plant-genomics-mcp, or the alternative claude mcp add plant-genomics -- uvx plant-genomics-mcp.
What does Plant Genomics do?
It's an MCP server that connects an agent to 23 plant gene databases, from Ensembl Plants and UniProt to KEGG and AlphaFold, exposing 56 tools for locus lookups, sequences, structures, pathways and homologs.
Does the server need anything installed beforehand?
Running it through uvx fetches the package on demand without manual setup; pipx, a Docker image and a from-source build are also available.
