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.

• 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 Ensembl's GraphQL integration.
• 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.

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

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 .

mcp dev rnacentral_sequence_search/server.py

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

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"
      ]
    }
  }
}

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

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

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

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

Find ncRNAs overlapping a specific gene in human:

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

Get the secondary structure diagram for a specific URS ID:

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

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
}

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

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

• 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.