Plant Genomics MCP Server

Other install paths (pipx, Docker, from source) Once connected, ask Claude a plain-language question - you don't have to name any tool or remember the chain. Its 34 documented tools cover locus, gene, interactions, bar. It runs locally over stdio via the published package.

People connecting this server to Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

VERIFIED ACTIVE

LAST COMMIT 2026-08-23 · ★ 3 · #142 OF 848 MAINTAINED OTHER · VERIFIED 2026-08-25

MIT · Python servers · how we verify → /methodology

01 · Install Plant Genomics

before you install - you'll need

Set PLANT_GENOMICS_MCP_LIVE, PLANT_GENOMICS_MCP_STDIO_SMOKE before connecting.

Claude Code

claude mcp add musharna-plant-genomics-mcp -- uvx plant-genomics-mcp

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "musharna-plant-genomics-mcp": {
      "command": "uvx",
      "args": [
        "plant-genomics-mcp"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license MIT - declared in the repository

pypi package plant-genomics-mcp - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.musharna is GitHub-verified and matches the repo owner

03 · What Plant Genomics can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can fetch gene record from Ensembl Plants REST (any plant species), fetch cross-DB references (UniProt, NCBI Gene, TAIR, GO, …) from Ensembl, fetch gene record from Phytozome BioMart (any Phytozome proteome), and resolve a locus to its UniProtKB record (Swiss-Prot preferred, TrEMBL OK).

Capability map

Tools grouped from the project's README - what Plant Genomics lets an agent do.

Locus

8 tools - e.g. Fetches gene record from Phytozome BioMart (any Phytozome proteome).; Resolves a locus to its UniProtKB record (Swiss-Prot preferred, TrEMBL OK).; Searches Europe PMC for papers mentioning the locus…

phytozome_lookup_locus · resolve_locus_to_uniprot · locus_literature · locus_go_annotations · tair_locus_info · plantcyc_locus_info…

Gene

4 tools - e.g. Fetches cross-DB references (UniProt, NCBI Gene, TAIR, GO, …) from Ensembl.; Fetches BAR ThaleMine + GAIA-aliases curator summary for an Arabidopsis locus.; ThaleMine curated GeneRIF statements…

get_gene_xrefs · bar_gene_summary · locus_gene_rifs · gene_report

Ensembl

2 tools - e.g. Fetches gene record from Ensembl Plants REST (any plant species).; Lists gene/transcript/cds/exon features overlapping a genomic interval (chr:start-end) via Ensembl /overlap/region - "what's in this QTL…

ensembl_plants_lookup_locus · ensembl_region_query

Bar

2 tools - e.g. Fetches BAR eFP-Browser expression profile (mean ± SD per tissue) for a locus.; Fetches BAR AIV interaction partners (Arabidopsis + rice) with confidence + papers.

bar_efp_expression · bar_aiv_interactions

Experimental

2 tools - e.g. PDBe experimentally-solved (X-ray / cryo-EM / NMR) structures for a locus (locus → UniProt): best-first PDB id, chain, method, resolution, coverage, residue spa; ThaleMine CURATED EXPERIMENTAL interaction…

experimental_structures · experimental_interactions

Blast

1 tool - e.g. NCBI BLAST URLAPI - async Put/Get polling with progress notifications.

blast_sequence

Gramene

1 tool - e.g. Fetches Gramene v69 homology entries (ortholog / paralog) with gene_tree_id.

gramene_homologs

Kegg

1 tool - e.g. Fetches KEGG pathway memberships. 7 organisms: Arabidopsis (ath:, native AGI), + rice (osa:), maize (zma:), soybean (gmx:), barley (hvg:), poplar (pop:), brachy

kegg_pathways

Latest releases

v1.21.0 · 2026-08-07

Still 50 tools / 23 backends - no tool, schema, or response-payload changes. A minor rather than a patch release because the supported SDK range moves: an environment that satisfied v1.20.0 may not satisfy this one.…

v1.20.0 · 2026-07-28

Still 50 tools / 23 backends - no new tools. A minor rather than a patch release because tools gain new parameters and response fields, and two tools change behaviour. · Added - provenance · Every backend is now…

v1.19.5 · 2026-07-28

No new tools or backends (still 50 tools / 23 backends), and no behaviour change to any · tool. Release cut so the repository can be archived to Zenodo and receive a DOI. · Added · CITATION.cff (CFF 1.2.0, validated…

04 · Who maintains Plant Genomics

Plant Genomics is maintained by musharna. We track 7 MCP servers from musharna - 7 actively maintained, 11 combined GitHub stars, oldest repo from May 2026. Full record: all servers from musharna.

  1. jobd Self-hostable GPU-aware job broker: submit, route by VRAM, babysit jobs across machines via MCP. ★ 4
  2. Data Aggregator Find & fetch research datasets across 17 archives, omics registries, and literature sources. ★ 2
  3. ldraw-mcp Render LDraw/LEGO models to images with real part geometry via headless Blender + ImportLDraw ★ 2

05 · Facts

repository
github.com/musharna/plant-genomics-mcp
website
https://github.com/musharna/plant-genomics-mcp
category
other - ranked #142 of 848 actively-maintained other servers as of 2026-08-25.
release cadence
10+ releases in the last 90 days (latest 2026-08-07)
registry
io.github.musharna/plant-genomics-mcp (active, first published 2026-05-24 · 16 versions)
packages
pypi:plant-genomics-mcp

06 · Plant Genomics FAQ

Is Plant Genomics still maintained?

Yes - as of 2026-08-25, its last commit was 2026-08-23 and it shipped 10+ releases in the last 90 days. We re-verify nightly.

What can Plant Genomics do?

With this server connected, an agent can fetch gene record from Ensembl Plants REST (any plant species), fetch cross-DB references (UniProt, NCBI Gene, TAIR, GO, …) from Ensembl, fetch gene record from Phytozome BioMart (any Phytozome proteome), and resolve a locus to its UniProtKB record (Swiss-Prot preferred, TrEMBL OK).

How do I install Plant Genomics?

Run `uvx plant-genomics-mcp`. The README documents 2 environment variables (PLANT_GENOMICS_MCP_LIVE, PLANT_GENOMICS_MCP_STDIO_SMOKE) to set first. Set PLANT_GENOMICS_MCP_LIVE, PLANT_GENOMICS_MCP_STDIO_SMOKE before connecting. You can also paste the ready-made client config above.

Does Plant Genomics run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Plant Genomics

Alternatives to Plant Genomics

Maintained other servers if Plant Genomics isn't the fit.

  1. Heyputer MCP Server Puter MCP enables AI tools to interact with Puter: manage files, websites, workers, and more ★ 43,204 · 2026-08-24
  2. Server Commands An MCP server to run arbitrary commands ★ 38,704 · 2026-08-05
  3. Zotero MCP (54yyyu) Search, read, annotate, and add to your Zotero research library, local or web. ★ 4,780 · 2026-08-25
  4. Firebase MCP Gives AI development tools Firebase-specific capabilities and expertise. ★ 4,460 · 2026-08-25
  5. Microsoft Fabric MCP Server MCP tools for interacting with Microsoft Fabric ★ 3,598 · 2026-08-21
  6. Ship Swift 40+ production-ready SwiftUI recipes for building full-stack iOS apps via MCP. ★ 2,968 · 2026-08-09

More MCP servers to compare · Toolradar · Pdfmux · Petsonality · Ambient Context MCP · Nauro

More Python MCP servers · Openshorts · Agent SUMO · Tesla · Better Code Review Graph · Better Telegram MCP · see all