Unofficial Ensembl MCP Server

by Augmented-Nature

173 downloads

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About

A comprehensive Model Context Protocol (MCP) server that provides access to the Ensembl REST API for genomic data, comparative genomics, and biological annotations.

Details

Author: Augmented-Nature
Downloads: 173
Categories: Other

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below

Plugin Name Unofficial Ensembl MCP Server

Command (node, npx, python, etc.)

Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

From the repository

Install dependencies with npm install, build with npm run build, then configure in Claude Desktop as an MCP server using the command node with arguments pointing to the built index.js. After setup, use natural language queries like "Look up the BRCA2 gene" to access genomic data.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "unofficial ensembl mcp server": {
            "ensembl": {
                "command": "node",
                "args": [
                    "/path/to/ensembl-server/build/index.js"
                ]
            }
        }
    }
}

McpServers

{
    "ensembl": {
        "command": "node",
        "args": [
            "/path/to/ensembl-server/build/index.js"
        ]
    }
}

Unofficial Ensembl MCP Server

A comprehensive Model Context Protocol (MCP) server that provides access to the Ensembl REST API for genomic data, comparative genomics, and biological annotations.

Developed by Augmented Nature

Overview

This server enables seamless access to Ensembl's vast genomic database through a standardized MCP interface. It supports gene lookups, sequence retrieval, variant analysis, comparative genomics, regulatory features, and much more across multiple species.

Features

Gene & Transcript Information

- Gene Lookup: Get detailed gene information by Ensembl ID or gene symbol
- Transcript Analysis: Retrieve all transcripts for a gene with structural details
- Gene Search: Search genes by name, description, or identifier with filtering options

Sequence Data

- Genomic Sequences: Extract DNA sequences for any genomic region or feature
- CDS Sequences: Get coding sequences for specific transcripts
- Sequence Translation: Translate DNA sequences to protein sequences
- Repeat Masking: Support for hard and soft repeat masking

Comparative Genomics

- Homolog Detection: Find orthologous and paralogous genes across species
- Phylogenetic Trees: Generate gene family trees in multiple formats
- Cross-Species Analysis: Compare genes and genomes across different organisms

Variant Data

- Variant Retrieval: Get genetic variants in genomic regions
- Consequence Prediction: Predict variant effects on genes and transcripts
- Population Genetics: Access allele frequencies and population data

Regulatory Features

- Regulatory Elements: Access enhancers, promoters, and TFBS data
- Motif Features: Get transcription factor binding motifs
- Cell Type Context: Filter regulatory features by cell type

Cross-References & Annotations

- External Database Links: Get cross-references to PDB, EMBL, RefSeq, etc.
- Coordinate Mapping: Convert coordinates between genome assemblies
- Ontology Terms: Access GO terms and functional annotations

Species & Assembly Information

- Species Lists: Browse available species and assemblies
- Assembly Statistics: Get genome assembly information and statistics
- Karyotype Data: Access chromosome information and banding patterns

Batch Processing

- Batch Gene Lookup: Process multiple genes simultaneously
- Batch Sequence Fetch: Retrieve sequences for multiple regions efficiently

Installation

```bash

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About

Details

Jump to

Setting up with Highlight

From the repository

Claude Desktop / Cursor

McpServers

Unofficial Ensembl MCP Server

Overview

Features

Gene & Transcript Information

Sequence Data

Comparative Genomics

Variant Data

Regulatory Features

Cross-References & Annotations

Species & Assembly Information

Batch Processing

Installation

Install

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