Plant genomics MCP server — 32 tools across 11 backends (Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR) + cross-source synthesis. stdio + Streamable-HTTP transports.
- ✓Open-source license (MIT)
- ✓Actively maintained (<30d)
- ✓Clear description
- ✓Topics declared
claude mcp add plant-genomics-mcp -- python -m -e{
"mcpServers": {
"plant-genomics-mcp": {
"command": "python",
"args": ["-m", "venv"]
}
}
}MCP Servers overview
# 🌱 plant-genomics-mcp > **50 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 + 12 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). [](https://pypi.org/project/plant-genomics-mcp/) [](https://github.com/musharna/plant-genomics-mcp/actions/workflows/test.yml) [](https://github.com/musharna/plant-genomics-mcp/actions/workflows/docker.yml)   [](https://glama.ai/mcp/servers/musharna/plant-genomics-mcp) <p align="center"> <img src="examples/assets/cc-demo.gif" alt="Claude Code answering a plant-genomics question live — calling plant-genomics-mcp across Ensembl Plants, UniProt, and Europe PMC and synthesizing the AT1G01010 / NAC1_ARATH gene profile in a single turn" width="780"> </p> ## 📦 Install ```bash pipx install plant-genomics-mcp claude mcp add plant-genomics --scope local -- plant-genomics-mcp ``` <details> <summary>Other install paths (Docker, from source)</summary> ```bash # 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" ``` </details> ## 💬 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. ## 🛠️ Tools **50 tools across 23 backends** — Ensembl Plants, Phytozome BioMart, UniProtKB, Europe PMC, QuickGO, Planteome, PlantCyc/PMN, g:Profiler, AlphaFold DB, PDBe, InterPro, JASPAR, PANTHER, OrthoDB, AraGWAS, 1001 Genomes, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, ThaleMine, BAR. 28 single-locus + 1 motif lookup + 1 region query + 1 variant annotator + 1 gene-set enrichment + 1 BLAST search + 12 parallel-batch + 5 cross-source synthesis. Most take a TAIR-style locus (e.g. `AT1G01010`) plus optional `organism=` (slug / scientific name / common name / NCBI taxid — 12-plant curated coverage matrix at the `pgmcp://organisms/coverage` MCP resource). All publish JSON `outputSchema` and EDAM ontology tags. <details> <summary>Full tool matrix</summary> | # | Category | Tool | What it does | | --- | ----------------------- | --------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | 1 | Gene metadata (live) | `ensembl_plants_lookup_locus` | Fetches gene record from Ensembl Plants REST (any plant species). | | 2 | Cross-references (live) | `get_gene_xrefs` | Fetches cross-DB references (UniProt, NCBI Gene, TAIR, GO, …) from Ensembl. | | 3 | Gene metadata (live) | `phytozome_lookup_locus` | Fetches gene record from Phytozome BioMart (any Phytozome proteome). | | 4 | Protein (live) | `resolve_locus_to_uniprot` | Resolves a locus to its UniProtKB record (Swiss-Prot preferred, TrEMBL OK). | | 5 | Literature (live) | `locus_literature` | Searches Europe PMC for papers mentioning the locus (free, no API key). | | 6 | GO annotations (live) | `locus_go_annotations` | Fetches QuickGO GO annotations (locus → UniProt → QuickGO). | | 7 | Sequence search (live) | `blast_sequence` | NCBI BLAST URLAPI — async Put/Get polling with progress notifications. | | 8 | Homology (live) | `gramene_homologs` | Fetches Gramene v69 homology entries (ortholog / paralog) with gene_tree_id. | | 9 | Pathways (live) | `kegg_pathways` | Fetches KEGG pathway memberships. 7 organisms: Arabidopsis (`ath:`, native AGI), + rice (`osa:`), maize (`zma:`), soybean (`gmx:`), barley (`hvg:`), poplar (`pop:`), brachypodium (`bdi:`) bridged via Ensembl → Entrez ID. | | 10 | Interactions (live) | `string_interactions` | Fetches STRING-DB first-neighbor interaction partners with per-channel score. | | 11 | Coexpression (live) | `atted_coexpression` | Fetches ATTED-II Ath-u.c4-0 top-N coexpression neighbors with z-scores. | | 12 | Curator summary (live) | `bar_gene_summary` | Fetches BAR ThaleMine + GAIA-aliases curator summary for an Arabidopsis locus. | | 13 | Expression (live) | `bar_efp_expression` | Fetches BAR eFP-Browser expression profile (mean ± SD per tissue) for a locus.
What people ask about plant-genomics-mcp
What is musharna/plant-genomics-mcp?
+
musharna/plant-genomics-mcp is mcp servers for the Claude AI ecosystem. Plant genomics MCP server — 32 tools across 11 backends (Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR) + cross-source synthesis. stdio + Streamable-HTTP transports. It has 3 GitHub stars and was last updated today.
How do I install plant-genomics-mcp?
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You can install plant-genomics-mcp by cloning the repository (https://github.com/musharna/plant-genomics-mcp) or following the README instructions on GitHub. ClaudeWave also provides quick install blocks on this page.
Is musharna/plant-genomics-mcp safe to use?
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Our security agent has analyzed musharna/plant-genomics-mcp and assigned a Trust Score of 87/100 (tier: Trusted). See the full breakdown of passed checks and flags on this page.
Who maintains musharna/plant-genomics-mcp?
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musharna/plant-genomics-mcp is maintained by musharna. The last recorded GitHub activity is from today, with 0 open issues.
Are there alternatives to plant-genomics-mcp?
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Yes. On ClaudeWave you can browse similar mcp servers at /categories/mcp, sorted by popularity or recent activity.
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