musharna/plant-genomics-mcp

Overview

A Model Context Protocol server that exposes 32 plant genomics tools across 11 backends including Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, and BAR. It supports stdio and Streamable-HTTP transports and can synthesize results across sources.

Best for

Best for
Developers building AI agents or pipelines that need unified access to plant genomics data

Use cases

• Query gene annotations and sequences from multiple plant genomics databases via a single interface
• Run BLAST searches against plant genomes and retrieve functional enrichment data
• Cross-reference gene identifiers and pathway data across Ensembl, KEGG, and STRING-DB

How to use

Install

pipx install plant-genomics-mcp

Tools exposed

• analyze_locus
• find_homologs
• biological_context
• streamable-HTTP
• PLANT_GENOMICS_MCP_HTTP_TOKEN
• PLANT_GENOMICS_MCP_NCBI_EMAIL
• PLANT_GENOMICS_MCP_HTTP_HOST
• PLANT_GENOMICS_MCP_HTTP_PORT
• PLANT_GENOMICS_MCP_HTTP_MAX_BODY
• PLANT_GENOMICS_MCP_HTTP_STATELESS
• PLANT_GENOMICS_MCP_HTTP_JSON
• PLANT_GENOMICS_MCP_BLAST_CONCURRENCY
• PLANT_GENOMICS_MCP_CACHE_TTL
• PLANT_GENOMICS_MCP_CACHE_SIZE
• PLANT_GENOMICS_MCP_CACHE_DISABLED
• ensembl_plants_lookup_locus
• get_gene_xrefs
• phytozome_lookup_locus
• resolve_locus_to_uniprot
• locus_literature

Tested with

Claude Code

Notes

A Model Context Protocol server that exposes 32 plant genomics tools across 11 backends including Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, and BAR. It supports stdio and Streamable-HTTP transports and can synthesize results across sources.

0 stars on GitHub. Last updated 2026-06-07. Licensed MIT.

Use cases

• Query gene annotations and sequences from multiple plant genomics databases via a single interface
• Run BLAST searches against plant genomes and retrieve functional enrichment data
• Cross-reference gene identifiers and pathway data across Ensembl, KEGG, and STRING-DB

Pros

• Covers a wide range of major plant genomics databases in one tool
• Supports both local stdio and HTTP streaming transports for flexible integration
• Cross-source synthesis reduces manual data merging

Cons

• Zero stars and no community traction yet
• Requires running a Python MCP server, adding deployment overhead
• Dependence on external APIs means reliability varies by backend uptime

Indexed from awesome-mcp-servers-punkpeye and enriched against its public facts.