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ensembl-database

Query the Ensembl REST API for gene lookups, sequences, and VEP variant analysis.

Updated Mar 15, 2026
Search Tags:#bioinformatics#genomics#sequence retrieval#variant analysis#ensembl#gene lookup
One-click install
npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill ensembl-database-sagunkayastha
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/sagunkayastha/claude_skills_collection/tree/main/scientific-databases/ensembl-database
Command: npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill ensembl-database-sagunkayastha

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ensembl_rest, requests, 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 query gene information, retrieve sequences, analyze variants, and perform comparative genomics without manual web browsing.

Core Features & Use Cases

  • Gene & Sequence Retrieval: Look up genes by symbol or ID, fetch DNA, transcript, or protein sequences.
  • Variant Analysis: Predict the functional impact of genetic variants using VEP.
  • Comparative Genomics: Find orthologs and paralogs across species.
  • Use Case: Automatically retrieve the protein sequence for a list of human gene symbols and then find their mouse orthologs.

Quick Start

Use the ensembl-database skill to look up gene information for 'BRCA2' in 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 from the Ensembl database using a REST API?▼

You can retrieve gene sequences from the Ensembl database by querying the REST API to look up genes by symbol or ID and fetch DNA, transcript, or protein sequences programmatically.

Can I find orthologs across species using the Ensembl REST API?▼

Yes, comparative genomics via the Ensembl REST API supports ortholog and paralog identification across over 250 species to facilitate cross-species sequence comparison.

What is the best way to predict functional impact of genetic variants in Ensembl?▼

The best way to predict the functional impact of genetic variants is by using the Variant Effect Predictor, or VEP, integrated within the Ensembl database REST API queries.

Does the Ensembl database Skill support programmatic integration with bioinformatics pipelines?▼

Yes, the Ensembl database Skill supports programmatic integration with genomic research pipelines by querying the Ensembl REST API directly using Python scripts and requests.

Why use programmatic Ensembl queries instead of manual web browsing for genomic research?▼

Programmatic Ensembl queries automate gene lookup, sequence retrieval, and variant analysis for large datasets, eliminating manual web browsing and streamlining bioinformatics workflows.

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