• ASSEMBLY
  • TRANSCRIPT
  • DATA
  • HUMAN

How to convert genomic coordinates with your AI

Connect Ensembl to your AI client to handle coordinate translations. Your agent maps locations across assemblies or transcript types instantly.

Ask AI about this page

Short answer

How do I convert genomic coordinates with my AI?

Your AI uses Ensembl to map coordinates between different assembly versions or between cDNA and genomic locations. You get precise mapping results without manual lookups.

Mapping outcomes

Where your data lands

The AI processes your requests into these specific results.

ASSEMBLY

Version mapping

The AI translates coordinates from an old assembly to a newer one. You get the updated positions for your specific genomic regions.

TRANSCRIPT

cDNA to genome

The AI maps cDNA sequences back to their genomic locations. This links transcript data directly to chromosomal coordinates.

DATA

Coordinate lists

The AI returns structured coordinate data. You can use these outputs for downstream analysis or visualization.

HUMAN

Manual validation

The AI provides the raw mapping, but you must verify the biological relevance of the translated coordinates for your specific study.

The workflow

What your AI does when the request arrives.

The AI acts as a bridge between your natural language and the Ensembl database.

  1. Identify mapping type

    Your agent determines if you need to move between assembly versions or link cDNA to a genome.

    get_mapget_map_cdna

  2. Query Ensembl

    The AI calls the necessary Ensembl tools to fetch the specific coordinate translations you asked for.

    get_mapget_map_cdna

  3. Format output

    The AI cleans up the raw data from the database into a readable format for your chat interface.

    get_map

  4. Deliver results

    The AI provides the mapped coordinates directly in your conversation.

    get_mapget_map_cdna

Try it

Copy these to start.

Use these prompts to trigger the Ensembl mapping tools.

Starting points

Swap out the bracketed text with your specific chromosome, position, or sequence details.

Ensembl Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp

Claude Desktop

Follow the steps below to connect in seconds.

  1. 1In Claude Desktop, open Settings → Connectors.
  2. 2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
  3. 3Click Add and start a new chat — Ensembl capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "ensembl-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/mcp"
    }
  }
}
Copy into chat04

  • Map the coordinates [chr1:100-200] from GRCh37 to GRCh38.

  • Convert this cDNA sequence [ATGC...] to its genomic coordinates.

  • Find the updated genomic positions for these coordinates in the latest assembly.

  • Map these cDNA locations to the genome using Ensembl.

  • Claude
  • ChatGPT
  • Cursor
  • VS Code
  • Windsurf
  • Claude Code
  • JetBrains
  • Cline

Start here

Connect Ensembl once, then ask.

Just link the Ensembl MCP to your client. Your credentials stay encrypted and you can start mapping immediately.

Connect Ensembl to your AI

FAQ

How this task behaves

  • 01

    Can the AI change the actual Ensembl database?

    No. The AI can only read and map data from Ensembl; it cannot write or modify any genomic records.

  • 02

    Does the AI handle both assembly and cDNA mapping?

    Yes, it uses specific tools to handle version-to-version mapping and cDNA-to-genomic mapping.

  • 03

    Can the AI perform complex sequence alignments?

    No. The AI is limited to the mapping capabilities provided by the Ensembl tools.

  • 04

    Will the AI automatically update my local files?

    No. The AI provides the mapped coordinates in the chat, but you must manually move that data into your files.

  • 05

    Can I map coordinates for any organism?

    The AI is limited to the organisms and assemblies supported by the Ensembl database.

  • More questions about Ensembl? See everything the Ensembl Connector can do

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