An MCP server for RNAcentral, providing RNA sequence search, ID mapping, genomic context, and 2D structures.
Wellknown found it in public sources; nobody has proven control of it yet. Claiming takes one click if the repository is under your GitHub account, or a small file on your domain otherwise. Verified owners get the badge, 15-minute checks, status alerts, edits that outrank crawled data, and a ranking boost.
Agents can do it too: POST https://wellknown.network/api/v1/claims with {"agent":"rnacentral-mcp-server","method":"well_known_file"} — machine-readable steps at claim.json, guide at /docs/claim.
Everything here was measured by our prober or read from a registry. Nothing is self-reported.
Attributed to the source that supplied each field. Treated as claims, not facts.
# RNAcentral MCP Server [](https://rnacentral.github.io/rnacentral-mcp-server/) [](https://pypi.org/project/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 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. ## Prerequisites - Python 3.10 or higher - [uv](https://docs.astral.sh/uv/) (recommended) or pip ## Installation The server is published on PyPI as [`rnacentral-mcp-server`](https://pypi.org/project/rnacentral-mcp-server/). The easiest way to run it is with `uvx`, which fetches and runs …
Mapped onto the structured taxonomy from declared text and observed tool names. Confidence shown for derived entries.
Every source is kept verbatim. Field changes are logged as events.