skills.rest
felixboehm
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ensembl-database

Queries the Ensembl genome database REST API for genes, sequences, and variants.

Updated Mar 10, 2026
Search Tags:#bioinformatics#genomics#sequence retrieval#variant analysis#ensembl#gene lookup
One-click install
npx skills add https://github.com/felixboehm/biochem-allergy --skill ensembl-database-felixboehm
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/ensembl-database
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill ensembl-database-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the Ensembl genome database, enabling researchers to retrieve gene information, sequences, variants, and comparative genomics data efficiently.

Core Features & Use Cases

  • Gene & Sequence Retrieval: Look up genes by symbol or ID, fetch DNA, transcript, or protein sequences.
  • Variant Analysis: Predict variant effects using VEP and query variation data.
  • Comparative Genomics: Find orthologs and paralogs across species.
  • Use Case: A researcher needs to find all known orthologs of the human BRCA2 gene in the mouse genome to study evolutionary conservation.

Quick Start

Use the ensembl-database skill to find orthologs for the human gene BRCA2 in the mouse species.

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 from the Ensembl REST API for genomic research?▼

To retrieve gene sequences from the Ensembl REST API, you can query the database using a gene symbol or ID to fetch corresponding DNA, transcript, or protein sequences directly into your analysis pipeline.

What is the best way to find orthologs for a specific gene across different species?▼

Finding orthologs across species involves querying the Ensembl comparative genomics database with a specific gene ID to identify evolutionary counterparts, such as locating all known orthologs of the human BRCA2 gene in the mouse genome.

Can I predict variant effects using VEP data from the Ensembl database?▼

Yes, you can predict variant effects by leveraging the Ensembl Variation Effect Predictor (VEP) API to query variation data and analyze the functional impact of genomic variants within your pipeline.

Does the Ensembl REST API support assembly coordinate mapping for over 250 species?▼

Yes, the Ensembl REST API supports assembly coordinate mapping and genomic data retrieval for over 250 species, allowing you to map genomic coordinates across different assembly versions.

Do I need the ensembl_rest package to perform gene lookups in Python?▼

Yes, performing gene lookups and interacting with the Ensembl REST API in Python requires the ensembl_rest and requests dependencies to facilitate the programmatic HTTP requests.

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