Plant Genomics MCP server

🌱 plant-genomics-mcp

52 tools for plant-genomics locus lookup over the Model Context Protocol —

28 single-locus + 1 motif lookup + 1 region query + 1 variant annotator + 1 gene-set enrichment + 1 BLAST search + 13 parallel-batch + 5 cross-source synthesis variants.

Free, public sources: Ensembl Plants, Phytozome BioMart, UniProtKB,

Europe PMC, QuickGO, Planteome, PlantCyc/PMN, g:Profiler, NCBI BLAST,

Gramene, JASPAR, KEGG, STRING-DB, ATTED-II, ThaleMine, and BAR (Bio-Analytic Resource for

Plant Biology).

📦 Install

# Zero-install — uv fetches and runs it on demand
claude mcp add plant-genomics --scope local -- uvx plant-genomics-mcp

Other install paths (pipx, Docker, from source)

# pipx — installs the CLI onto your PATH
pipx install plant-genomics-mcp
claude mcp add plant-genomics --scope local -- plant-genomics-mcp

# GHCR Docker image
docker pull ghcr.io/musharna/plant-genomics-mcp:latest
claude mcp add plant-genomics --scope local -- \
  docker run --rm -i ghcr.io/musharna/plant-genomics-mcp:latest

# From source
git clone https://github.com/musharna/plant-genomics-mcp.git
cd plant-genomics-mcp
python -m venv .venv && .venv/bin/pip install -e .
claude mcp add plant-genomics --scope local -- "$(pwd)/.venv/bin/plant-genomics-mcp"

💬 Try it

Once connected, ask Claude a plain-language question — you don't have to name any tool or remember the chain:

**"Tell me everything about the Arabidopsis gene AT1G01010 — its

function, GO terms, KEGG pathways, protein-interaction partners, and

recent papers."**

Claude fans out across Ensembl Plants, UniProt, QuickGO, KEGG, STRING-DB, and Europe PMC in a single turn and hands back one synthesized answer. Swap in any locus and pass organism= for cross-species — e.g. rice Os01g0100100 (oryza_sativa) — and it routes to the right backends automatically.

A worked 64-call run over 114 genes in three organisms, with the 60 gaps it logged (27 since closed), is in examples/arf_family/PAGE.md.

🛠️ Tools

Shortened. The full README is on GitHub.