RNAcentral MCP Server

This is an MCP server that provides a comprehensive interface to the RNAcentral database, allowing for complex searches, sequence mapping, genomic analysis, and metadata retrieval for non-coding RNA sequences.

📖 Full documentation: https://rnacentral.github.io/rnacentral-mcp-server/ — installation guides for Claude Desktop / Claude Code / other MCP clients, per-tool reference, and examples.

Features

• Comprehensive Search: Query RNAcentral using natural language or filters (RNA type, taxon, expert database). Combines EBI Search and RNAcentral API data for enriched metadata (Rfam hits, GO annotations).
• Sequence Search: Search for RNA sequences across multiple databases to find identical or similar entries.
• Bidirectional ID Mapping: Map between RNAcentral URS IDs and external database identifiers (miRBase, Ensembl, HGNC, etc.) with automatic taxonomy resolution.
• Bulk Sequence Export: Export search results in FASTA or Parquet formats, ideal for downstream analysis or machine learning datasets.
• Genomic Overlap (Ensembl): Find non-coding RNAs overlapping specific genomic coordinates or gene symbols using the Ensembl REST API.
• 2D Structure Diagrams: Retrieve secondary structure (2D) diagrams in SVG format for RNAs with known or predicted folds.
• Literature Summaries: Access AI-generated literature summaries for RNA sequences to understand their biological context.

Prerequisites

• Python 3.10 or higher
• uv (recommended) or pip

Installation

The server is published on PyPI as rnacentral-mcp-server. The easiest way to run it is with uvx, which fetches and runs it without a manual install:

uvx --from rnacentral-mcp-server run-server

Or install it into an environment with pip / uv:

pip install rnacentral-mcp-server
# or
uv add rnacentral-mcp-server

This makes the run-server console script available.

From source (for development)

1. Set up a Python environment:

# Using uv (recommended)
uv venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

# Add dependencies
uv add "mcp[cli]" aiohttp

2. Install the package in editable mode:

uv pip install -e .

Running the Server

Development Mode (with MCP Inspector)

mcp dev rnacentral_sequence_search/server.py

This will start the server and open the MCP Inspector, allowing you to test the server interactively.

Using with Claude Desktop

To install the server in Claude Desktop, add this to your claude_desktop_config.json. You can optionally specify a --log-dir to save logs to a specific directory:

{
  "mcpServers": {
    "rnacentral": {
      "command": "uvx",
      "args": [
        "--from",
        "rnacentral-mcp-server",
        "run-server",
        "--log-dir",
        "/Users/YOUR_USERNAME/logs/rnacentral"
      ]
    }
  }
}

(To run the latest unreleased code instead, replace rnacentral-mcp-server with git+https://github.com/rnacentral/rnacentral-mcp-server.git.)

Direct Execution

You can run the server directly using Python. Use the --log-dir argument to specify where to save log files:

python rnacentral_sequence_search/server.py --log-dir ./logs

Or using the installed script:

run-server --log-dir ./logs

Usage Examples

Once the server is running, you can interact with various tools:

Bidirectional ID Mapping

Map an external ID to RNAcentral and see all cross-references:

Tool: map_rna_id
Arguments:
{
  "identifier": "MIMAT0000062",
  "taxon": "Homo sapiens"
}

Genomic Overlap

Find ncRNAs overlapping a specific gene in human:

Tool: get_overlapping_ncrnas
Arguments:
{
  "species": "human",
  "gene_symbol": "HOTAIR"
}

2D Structure Retrieval

Get the secondary structure diagram for a specific URS ID:

Tool: get_secondary_structure_svg
Arguments:
{
  "urs_id": "URS0000049E57"
}

Bulk Sequence Export

Export a set of sequences matching a search query for machine learning:

Tool: export_sequences
Arguments:
{
  "query": "lncRNA",
  "taxon": "9606",
  "format": "parquet",
  "max_length": 500
}

Literature Summaries

Get a summary of the known biological role of an RNA:

Tool: get_rna_description
Arguments:
{
  "rna_id": "mmu-mir-191"
}

Notes

• The server handles complex queries by orchestrating multiple upstream APIs (EBI Search, RNAcentral, Ensembl).
• Sequence searches poll for results with a timeout to handle varying server loads.
• The 2D structure SVG can be used for direct visualization in supporting clients.
• For very large exports, use the export_sequences tool which uses specialized microservices for efficiency.