skills.rest
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ensembl-database

Query Ensembl REST for gene, sequence, and variant data across 250+ species.

94|11|Updated Mar 26, 2026
Search Tags:#genomics#orthologs#rest-api#ensembl#variant-analysis#gene-lookup#sequence-retrieval
One-click install
npx skills add https://github.com/swaruplab/operon --skill ensembl-database-swaruplab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/swaruplab/operon/tree/main/src-tauri/protocols/ensembl-database
Command: npx skills add https://github.com/swaruplab/operon --skill ensembl-database-swaruplab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Researchers need programmatic access to Ensembl data for gene information, sequences, and variants to power reproducible analyses and pipelines across 250+ species.

Core Features & Use Cases

  • Gene Information Retrieval: look up genes by symbol or Ensembl ID, retrieve coordinates, transcripts, and cross-references.
  • Sequence & Variant Analysis: fetch genomic sequences and run variant effect predictions, plus access orthologs across species.
  • Use Case: Integrate Ensembl data into a pipeline to build gene-centric reports with coordinates, sequences, and predicted variant consequences.

Quick Start

Ask Ensembl REST to retrieve BRCA2 gene information and its DNA sequence for human.

Frequently Asked Questions about ensembl-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve gene sequences and coordinates from the Ensembl REST API?▼

To retrieve gene sequences and coordinates from the Ensembl REST API, query by gene symbol or Ensembl ID to fetch transcripts, cross-references, and genomic sequences across 250+ species. The tool manages REST endpoints, rate limiting, and error handling automatically.

Can I perform variant effect prediction and ortholog analysis using Ensembl data?▼

Yes, you can perform variant effect prediction and ortholog analysis using Ensembl data by fetching genomic sequences and running variant predictions alongside cross-species ortholog retrieval for comparative genomics workflows.

Does this Ensembl REST tool handle rate limiting and coordinate mapping between assemblies?▼

Yes, this Ensembl REST tool handles rate limiting and error handling, while also applying coordinate mapping between assemblies to ensure accurate genomic sequence retrieval and variant data alignment.

What's the best way to look up human gene information like BRCA2 programmatically?▼

The best way to look up human gene information like BRCA2 programmatically is querying the Ensembl REST API by gene symbol to retrieve coordinates, transcripts, and cross-references for building gene-centric reports.

Do I need the requests library to fetch genomic sequences and variant data?▼

Yes, you need the requests library as a dependency to fetch genomic sequences and variant data, enabling Python-based programmatic access to Ensembl REST endpoints for gene lookup and comparative genomics.

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