RNAcentral MCP Server

This is an MCP server that wraps the RNAcentral sequence search API, allowing you to easily search for RNA sequences and get nicely formatted results.

Features

• Bidirectional ID Mapping: Map between RNAcentral URS IDs and external database identifiers (miRBase, Ensembl, HGNC, etc.).
• Comprehensive Search: Query RNAcentral using natural language or filters (RNA type, taxon, expert database).
• Metadata Enrichment: Results include Rfam hits, GO annotations, and 2D structure availability.
• Sequence Search: Search for RNA sequences across multiple databases with progress tracking.
• Markdown Results: Formatted results with links to RNAcentral entries and external resources.

Prerequisites

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

Installation

1. Set up a Python environment:

# Using uv (recommended)
uv init rnacentral-mcp
cd rnacentral-mcp
uv venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

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

Or using pip:

# Using pip
pip install "mcp[cli]" aiohttp

2. Save the rnacentral_sequence_search/server.py file to your project directory.

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",
        "git+https://github.com/rnacentral/rnacentral-mcp-server.git",
        "run-server",
        "--log-dir",
        "/Users/YOUR_USERNAME/logs/rnacentral"
      ]
    }
  }
}

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

Or via the MCP CLI:

mcp run rnacentral_sequence_search/server.py

Usage Examples

Once the server is running, you can search for RNA sequences:

Bidirectional ID Mapping

Map an external ID to RNAcentral and see all cross-references (optionally filtered by taxon name or ID):

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

Comprehensive Search

Search for RNAs with specific criteria (e.g., human telomerase RNAs with 2D structure):

Tool: query_rnacentral
Arguments:
{
  "query": "telomerase",
  "taxon": "Homo sapiens",
  "has_secondary_structure": true
}

Basic sequence search

Search for an RNA sequence across all databases:

Tool: search_sequence
Arguments:
{
  "sequence": "ACCGUGCAAUCGAUGCAU"
}

Search specific databases

Search for a sequence in specific databases:

Tool: search_sequence
Arguments:
{
  "sequence": "ACCGUGCAAUCGAUGCAU",
  "databases": ["miRBase", "snoDB"]
}

Notes

• The server polls the RNAcentral API for up to 30 attempts with 2-second intervals between attempts.
• For very large sequences or during high server load, searches might time out.
• The results display the top 5 hits by default, with links to the full results on the RNAcentral website.