ensembl-database

Query Ensembl REST endpoints for gene, sequence, variant, and orthology data.

1|Updated Mar 4, 2026

Search Tags:#genomics #orthologs #ensembl #assembly-mapping #variant-analysis #data-retrieval

Ready to run

npx skills add https://github.com/Hung-3008/agusta --skill ensembl-database-hung-3008

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/ensembl-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill ensembl-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Query Ensembl REST endpoints to fetch gene, sequence, variant, and orthology data across species.

Core Features & Use Cases

Gene information retrieval by symbol or Ensembl ID
Sequence retrieval for DNA, transcripts, and proteins
Variant analysis with VEP and cross-species orthology mapping
Use Case: Retrieve BRCA2 details in human, then obtain its orthologs for comparative genomics
Use Case: Map coordinates between GRCh37 and GRCh38 to coordinate with older datasets

Quick Start

Ask Ensembl for BRCA2 in human to retrieve gene data, sequences, and variant predictions.

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 orthologs across species using Ensembl?▼

To retrieve gene sequences and orthologs across species, query the Ensembl REST endpoints to fetch gene data by symbol or Ensembl ID. You can obtain DNA, transcripts, and proteins, then map cross-species orthology for comparative genomics.

Can I map genomic coordinates between GRCh37 and GRCh38 assembly versions?▼

Yes, you can map genomic coordinates between GRCh37 and GRCh38 assembly versions. The Skill queries Ensembl REST endpoints to perform assembly mapping, allowing you to align and coordinate older datasets with current genome builds.

How do I perform variant analysis and VEP predictions on vertebrate genomes?▼

You can perform variant analysis and VEP predictions on vertebrate genomes by querying the Ensembl REST endpoints. The Skill fetches variant data and applies Variant Effect Predictor logic to retrieve detailed predictions for genomic variants.

Does the Ensembl data retrieval tool support batch requests and rate limiting for production use?▼

Yes, the Ensembl data retrieval tool supports batch requests and rate limiting for production use. It implements robust error handling and batch endpoint support to ensure reliable querying of gene, sequence, and variant data across species.

What is the best way to look up gene information by symbol or Ensembl ID?▼

The best way to look up gene information by symbol or Ensembl ID is to query the Ensembl REST endpoints. This retrieves comprehensive gene details, sequence data, and variant predictions for vertebrate genomes directly.

Why do I need assembly mapping when working with older genomic datasets?▼

You need assembly mapping when working with older genomic datasets because genome builds like GRCh37 and GRCh38 use different coordinate systems. Mapping coordinates between assemblies ensures accurate region overlaps and gene data alignment with current references.