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ensembl-database

Retrieve genomic data from the Ensembl REST API using Python.

Updated Dec 17, 2025
Search Tags:#sequence retrieval#variant analysis#ensembl#gene lookup#genomic research
One-click install
npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill ensembl-database-robotlearning123
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/ensembl-database
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill ensembl-database-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill simplifies accessing and querying the Ensembl genome database for genomic research, providing efficient ways to retrieve gene information, sequences, variants, and perform comparative genomics.

Core Features & Use Cases

  • Gene Information Retrieval: Lookup genes by symbol, Ensembl ID, or external identifiers.
  • Sequence Retrieval: Fetch DNA, transcript, or protein sequences in various formats.
  • Variant Analysis: Analyze genetic variants using the Variant Effect Predictor (VEP).
  • Comparative Genomics: Perform cross-species comparisons to identify orthologs and paralogs.
  • Use Case: A researcher could use this Skill to quickly find gene information and sequence data for a specific gene of interest.

Quick Start

Use the ensembl-database skill to retrieve gene information for 'BRCA2' in the human genome.

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 information from the Ensembl genome database using Python?▼

Gene information retrieval from the Ensembl genome database is done by accessing the Ensembl REST API to lookup genes by symbol, Ensembl ID, or external identifiers and fetch associated genomic data.

Can I analyze genetic variants using the Variant Effect Predictor with Ensembl REST API?▼

Variant analysis in Ensembl is performed using the Variant Effect Predictor (VEP) via the REST API to analyze genetic variants and determine their functional effects on genes and transcripts.

What's the best way to perform cross-species comparative genomics to identify orthologs and paralogs?▼

Comparative genomics to identify orthologs and paralogs is performed by querying the Ensembl REST API to retrieve cross-species genomic data and compare evolutionary relationships between genes.

Do I need the ensembl_rest Python library to fetch genomic data from the Ensembl database?▼

The ensembl_rest Python library is required to interact with the Ensembl REST API for retrieving genomic data including gene sequences, variants, and comparative genomics information.

How do I lookup a gene like BRCA2 in the human genome using Ensembl identifiers?▼

Gene lookup for BRCA2 in the human genome is performed by querying the Ensembl REST API with the gene symbol or Ensembl ID to retrieve gene information, sequences, and variant data.

What types of sequences can I retrieve when querying the Ensembl genome database?▼

Sequence retrieval from the Ensembl genome database supports fetching DNA, transcript, and protein sequences in various formats to support biological research and variant analysis.

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