Plant Genomics
Plant genomics MCP — 58 tools across 24 backends with cross-source synthesis.
Installation
Ajoutez ceci à la configuration MCP de votre client (Claude Desktop : claude_desktop_config.json ; Cursor : .cursor/mcp.json ; VS Code et les autres utilisent la même forme « mcpServers »).
plant-genomics-mcpclaude mcp add plant-genomics -- uvx plant-genomics-mcp==1.30.0{
"mcpServers": {
"plant-genomics": {
"command": "uvx",
"args": [
"plant-genomics-mcp==1.30.0"
]
}
}
}Documentation
Tirée du README du projet sur GitHub, actualisée chaque semaine. Les liens ouvrent GitHub.
plant-genomics-mcp
plant-genomics-mcp is an MCP server that lets AI agents look up plant genes in 23 free public databases, from Ensembl Plants and UniProt to KEGG, STRING and AlphaFold, with curated coverage of 12 plants.
Does it help?
Yes, over Claude alone, which declined most lookups. Against web search it is not measurably more accurate, on single lookups or on harder multi-step ones.
Claude Opus 5.5, in Claude Code, answered 52 plant gene-lookup questions three times each: 151 of 156 right with web search, 156 of 156 with the server, not separated (4 questions against 0, McNemar p = 0.125). On 36 harder questions (orthologs then coordinates, ID mapping, genes in an interval; re-run 2026-10-18) both got all 108 right; the server was faster at the median (0.77×, 95% CI 0.64 to 0.96) and dearer (1.72×, 1.46 to 2.24). The key comes from the databases the server reads, so this tests the lookups, not whether those databases are right.
Method, controls and limitations: benchmarks/agent_qa.
Install
# uv fetches and runs it on demand
claude mcp add plant-genomics --scope local -- uvx plant-genomics-mcpOther 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
Ask in plain language; the client picks the tools:
"Tell me everything about the Arabidopsis gene AT1G01010 — its function, GO terms, KEGG pathways, protein-interaction partners, and recent papers."
For another species, name it or pass organism= (e.g. rice Os01g0100100,
oryza_sativa). A recorded ortholog run, where Claude checked three sources
and said which one does not back the rice match:
Prompts and full answers for both screenshots: examples/assets/cards/RUN.md.
A worked 64-call run over 114 genes in three organisms, with the 51 gaps it
logged (39 since closed), is in examples/arf_family/PAGE.md.
Per-tool walkthroughs, including the one-call gene dossier
gene_report_AT1G01010.md, are in
examples/.
Tools
56 tools across 23 backends:
| Area | Tools |
|---|---|
| Gene records | ensembl_plants_lookup_locus, phytozome_lookup_locus, get_gene_xrefs, bar_gene_summary, tair_locus_info |
| Sequence | get_sequence, blast_sequence |
| Protein and structure | resolve_locus_to_uniprot, interpro_domains, alphafold_structure, experimental_structures |
| Function | locus_go_annotations, locus_plant_ontology, locus_gene_rifs, go_enrichment, locus_literature |
| Pathways | kegg_pathways, plantcyc_locus_info |
| Interactions and expression | string_interactions, experimental_interactions, bar_aiv_interactions, atted_coexpression, bar_efp_expression |
| Homology and families | gramene_homologs, ensembl_plants_paralogs, orthodb_orthologs, panther_family, gene_tree_members, entry_members |
| TF motifs | tf_binding_motifs, jaspar_motif |
| Variation | locus_variants, vep_annotate, aragwas_associations, arabidopsis_natural_variation |
| Regions and assemblies | ensembl_region_query, ensembl_plants_assembly |
| Provenance | upstream_release |
| Batch and synthesis | batch_* (12), batch_locus_call, *_synth (3), consensus_homologs, gene_report |
Most take a locus (e.g. AT1G01010) and an optional organism=. Every tool is
marked read-only. What each tool does, the list of backends, the MCP resources
and prompts, all environment variables and the error model:
docs/reference.md.
Configuration
stdio (plant-genomics-mcp, the default) needs no configuration.
plant-genomics-mcp-http serves streamable HTTP at http://host:port/mcp;
there is no public endpoint, so you run it yourself, behind your own token.
| Variable | When | Effect |
|---|---|---|
PLANT_GENOMICS_MCP_HTTP_TOKEN | HTTP transport only | Bearer token for /mcp; must be ≥32 chars or the HTTP server aborts at startup. Generate openssl rand -hex 32. |
PLANT_GENOMICS_MCP_NCBI_EMAIL | If you use BLAST | NCBI etiquette contact. Unset → placeholder + per-call warning; NCBI may throttle. |
Development
.venv/bin/pip install -e '.[dev]' # or: uv sync --extra dev
.venv/bin/pytest -q # unit tests
PLANT_GENOMICS_MCP_LIVE=1 .venv/bin/pytest -q # adds live network probes
PLANT_GENOMICS_MCP_STDIO_SMOKE=1 .venv/bin/pytest -q # adds stdio smoke
.venv/bin/ruff check .A bare uv sync omits the test dependencies. CI runs the unit suite and the
stdio smoke on Python 3.11–3.14 with the network blocked. A weekly job checks
27 loci against a frozen snapshot and pages on drift
(docs/benchmarking.md). Setup: CONTRIBUTING.md.
Release notes: CHANGELOG.md.
License
MIT, see LICENSE. The underlying services (Ensembl Plants,
Phytozome, TAIR, PlantCyc, BAR) have their own terms of use; check them before
bulk querying.
Questions fréquentes
Qu'est-ce que Plant Genomics ?
Plant genomics MCP — 58 tools across 24 backends with cross-source synthesis.
Comment installer Plant Genomics ?
Il s'exécute sur votre machine. Dans Claude Code : claude mcp add plant-genomics -- uvx plant-genomics-mcp==1.30.0. Pour les autres clients, collez la configuration JSON de cette page dans leurs réglages MCP.
Faut-il une clé API pour Plant Genomics ?
Son entrée au registre n'indique aucune clé ni secret obligatoire. Certaines fonctions peuvent tout de même demander un compte auprès du service auquel il se connecte.
Plant Genomics est-il open source ?
Oui. Son code est sur GitHub sous licence MIT.
Qui maintient Plant Genomics ?
Il est publié par musharna. AI.tn le référence sans le maintenir ni le recommander.
Issu du registre MCP officiel. Être listé n'est pas une recommandation : vérifiez le code et les permissions d'un serveur avant de lui donner accès à vos données.