• DATA
  • ANALYSIS
  • EXPORT
  • HUMAN

How to identify orthologous genes with your AI

Connect Ensembl to your AI client to automate homology searches. Once linked, your agent handles the heavy lifting of finding equivalent genes across different species.

Ask AI about this page

Short answer

How can I find orthologous genes using AI?

Your AI uses the Ensembl connector to run homology searches across species. It identifies equivalent genes and maps their evolutionary relationships. You'll get a structured list of orthologs ready for analysis.

The results you get.

Where your data lands.

The AI processes your queries and organizes the findings into these specific outputs.

DATA

Homology lists

The AI pulls direct ortholog matches from Ensembl. You get a clean list of gene equivalents across your target species.

ANALYSIS

Conservation maps

Your agent identifies conserved regions and evolutionary patterns. This helps you pinpoint which gene functions are most stable across lineages.

EXPORT

Structured tables

The AI formats the gene identifiers and species data into tables. You can move these straight into your downstream bioinformatics tools.

HUMAN

Manual validation

The AI flags high-confidence matches, but you decide which orthologs are biologically relevant. You handle the final interpretation of the evolutionary data.

The workflow

What your AI does when a homology request arrives.

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

  1. Query translation

    Your agent takes your species names and gene identifiers and prepares them for the Ensembl database.

    get_homology

  2. Database execution

    The AI triggers the homology search to find matching gene sequences across the requested genomes.

    get_homology

  3. Data structuring

    The agent parses the raw homology data into a readable format, grouping matches by species and sequence similarity.

    get_homology

  4. Result filtering

    The AI filters the results based on your specific conservation criteria or similarity thresholds.

    get_homology

Try it

Copy these to start.

Use these prompts to kick off your search.

Starting points

Swap out the bracketed species and gene names for your actual research targets.

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

  • Find the orthologs for the human BRCA1 gene in mouse and zebrafish.

  • Run a homology search for the insulin receptor across all available mammalian species.

  • Identify equivalent genes for the Arabidopsis thaliana gene At1g01010 in various plant species.

  • List all orthologous genes for the human ACE2 gene in primates.

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

Start here

Connect Ensembl once, then ask.

Just click the link to connect the Ensembl MCP to your client. Your credentials stay encrypted, and you can start querying immediately.

Connect Ensembl to your AI

FAQ

How this task behaves.

  • 01

    Can the AI perform custom sequence alignments?

    No. The AI relies on the homology tools provided by Ensembl to find existing orthologs.

  • 02

    Will the AI change any data in my Ensembl account?

    No. The AI only reads data from Ensembl to perform searches; it cannot modify the database.

  • 03

    Can I use this to find paralogs instead of orthologs?

    Yes, if you specify that you are looking for gene duplications within the same species in your prompt.

  • 04

    Does the AI handle the biological interpretation?

    No. The AI finds the matches and organizes the data, but you must interpret the evolutionary significance.

  • 05

    Can the AI download large genomic files?

    No. The AI is designed to retrieve specific gene homology information, not to act as a bulk genome downloader.

  • More questions about Ensembl? The Connector page answers them. See everything the Ensembl Connector can do

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