# Ensembl

> Use this tool when you need to access Ensembl's genomic database for bioinformatics research, leveraging 20+ specialized tools for gene lookup, sequence retrieval, and variant analysis. It solves problems in comparative genomics, regulatory feature analysis, and phylogenetic data retrieval, accepting gene or sequence inputs and returning annotated data through a REST API interface. Ideal for research applications requiring programmatic access to genomic data, it provides both individual and batch processing capabilities for efficient analysis.

Canonical page: https://skillsregistry.net/skills/augmented-nature-ensembl  
JSON: https://api.skillsregistry.net/v1/skills/augmented-nature-ensembl

## Description

Production-ready MCP server built by Augmented Nature that provides AI assistants with complete access to Ensembl's genomic database through 20+ specialized tools covering gene lookup, sequence retrieval, comparative genomics, variant analysis, and regulatory features. The implementation uses TypeScript with comprehensive input validation and error handling, offering both individual tools (gene search, homolog finding, transcript analysis) and batch processing capabilities for multiple genes or sequences simultaneously. Designed for bioinformatics workflows, the server integrates directly with Ensembl's REST API to support research applications requiring programmatic access to gene annotations, phylogenetic data, variant consequences, and cross-species comparative analysis across all Ensembl-supported organisms.

## Trust

- **Trust score (0–1):** 0.99
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** database
- **Updated:** 2026-09-28

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/augmented-nature-ensembl)
- **Repository:** <https://github.com/augmented-nature/ensembl-mcp-server>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "augmented-nature-ensembl"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/augmented-nature-ensembl` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/augmented-nature-ensembl/pull`

---
SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt