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ensembl-database

Query gene annotations, sequences, and variants from Ensembl REST API.

Updated May 10, 2026
Search Tags:#genomics#gene annotation#comparative genomics#sequence retrieval#variant analysis#ensembl
One-click install
npx skills add https://github.com/Imad-Oute/ResearchForge --skill ensembl-database-imad-oute
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/Imad-Oute/ResearchForge/tree/main/OpenSource-Projects/claude-scientific-skills/scientific-skills/ensembl-database
Command: npx skills add https://github.com/Imad-Oute/ResearchForge --skill ensembl-database-imad-oute

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill enables researchers to query and retrieve detailed genomic information from the Ensembl database, facilitating constant access to vital genetic and genomic data.

Core Features & Use Cases

  • Gene Data Retrieval: Look up gene information, transcripts, and protein sequences by gene symbols or Ensembl IDs.
  • Sequence and Variant Analysis: Download DNA, transcript, or protein sequences and predict variant effects using VEP.
  • Comparative Genomics and Mapping: Find orthologs across species and convert coordinates between genome assemblies.
  • Use Case: A geneticist wants to get the sequence of a gene, find its ortholog in mice, and assess the impact of specific mutations.

Quick Start

Use the ensembl-database skill to look up gene information by symbol and retrieve its DNA sequence.

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 annotations from the Ensembl database?▼

To retrieve Ensembl gene sequences and annotations, query the database by gene symbols or Ensembl IDs to download DNA, transcript, or protein sequences and look up detailed gene information.

Can I find orthologs across species using comparative genomics data?▼

Yes, you can find orthologs across species by using comparative genomics features to map and retrieve homologous gene data between different organisms.

How do I predict variant effects on gene transcripts?▼

You can predict variant effects on gene transcripts by running variant effect prediction (VEP) on retrieved sequences to assess the impact of specific mutations.

Do I need the ensembl_rest package and network access to query genomic data?▼

Yes, you need the ensembl_rest package and active network access to Ensembl REST API endpoints to query genomic data, retrieve sequences, and perform variant analysis.

Can I convert coordinates between different genome assemblies?▼

Yes, you can convert coordinates between genome assemblies using the comparative genomics and mapping functionalities to translate positional data across reference genomes.

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