{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_hp6grcf3yucs","handle":"rnacentral-mcp-server","url":"https://wellknown.network/agents/rnacentral-mcp-server","links":{"self":"https://wellknown.network/agents/rnacentral-mcp-server/record.json","html":"https://wellknown.network/agents/rnacentral-mcp-server","markdown":"https://wellknown.network/agents/rnacentral-mcp-server/record.md","api":"https://wellknown.network/api/v1/agents/rnacentral-mcp-server","status":"https://wellknown.network/api/v1/agents/rnacentral-mcp-server/status","claim":"https://wellknown.network/agents/rnacentral-mcp-server/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/rnacentral-mcp-server/claim.json","badge":"https://wellknown.network/agents/rnacentral-mcp-server/badge.svg","openapi":"https://wellknown.network/openapi.json"},"ard":{"identifier":"urn:air::server:rnacentral-mcp-server","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"rnacentral-mcp-server","summary":"An MCP server for RNAcentral, providing RNA sequence search, ID mapping, genomic context, and 2D structures.","description":"# RNAcentral MCP Server\n\n[![Documentation](https://img.shields.io/badge/docs-github%20pages-blue)](https://rnacentral.github.io/rnacentral-mcp-server/)\n[![PyPI](https://img.shields.io/pypi/v/rnacentral-mcp-server)](https://pypi.org/project/rnacentral-mcp-server/)\n\nThis 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.\n\n📖 **Full documentation:** <https://rnacentral.github.io/rnacentral-mcp-server/> — installation guides for Claude Desktop / Claude Code / other MCP clients, per-tool reference, and examples.\n\n## Features\n\n- **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).\n- **Sequence Search**: Search for RNA sequences across multiple databases to find identical or similar entries.\n- **Bidirectional ID Mapping**: Map between RNAcentral URS IDs and external database identifiers (miRBase, Ensembl, HGNC, etc.) with automatic taxonomy resolution.\n- **Bulk Sequence Export**: Export search results in FASTA or Parquet formats, ideal for downstream analysis or machine learning datasets.\n- **Genomic Overlap (Ensembl)**: Find non-coding RNAs overlapping specific genomic coordinates or gene symbols using Ensembl's GraphQL integration.\n- **2D Structure Diagrams**: Retrieve secondary structure (2D) diagrams in SVG format for RNAs with known or predicted folds.\n- **Literature Summaries**: Access AI-generated literature summaries for RNA sequences to understand their biological context.\n\n## Prerequisites\n\n- Python 3.10 or higher\n- [uv](https://docs.astral.sh/uv/) (recommended) or pip\n\n## Installation\n\nThe 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 …","publisher":null,"homepage":"https://github.com/RNAcentral/rnacentral-mcp-server","repository":"https://github.com/RNAcentral/rnacentral-mcp-server","version":"0.1.1","license":"MIT License  Copyright (c) 2026 RNAcentral  Permission is hereb…","protocols":["mcp"],"tags":["bioinformatics","mcp","model-context-protocol","rna","rnacentral"],"pricing":null,"endpoints":[{"url":"pypi:rnacentral-mcp-server","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","license":"pypi","repoUrl":"pypi","summary":"pypi","version":"pypi","description":"pypi","homepageUrl":"pypi"}},"derived":{"capabilities":[{"slug":"data.database","name":"Databases","confidence":0.791,"provenance":"derived"},{"slug":"dev.docs-lookup","name":"Documentation Lookup","confidence":0.791,"provenance":"derived"}],"categories":["data","dev"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"rnacentral-mcp-server","registry":"pypi","observedAt":"2026-09-10T11:28:32.294Z","publishedAt":"2026-06-04T13:09:56.273416Z","latestVersion":"0.1.1"}},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"rnacentral-mcp-server","url":"https://pypi.org/project/rnacentral-mcp-server/","firstSeenAt":"2026-09-10T11:27:12.519Z","fetchedAt":"2026-09-10T11:27:12.519Z","normalizedAt":"2026-09-10T11:27:12.519Z"}]},"firstSeenAt":"2026-09-10T11:27:12.519Z","updatedAt":"2026-09-10T11:28:32.294Z"}