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db-ensembl

Query the Ensembl REST API for gene lookups, sequences, and variants.

Updated Mar 13, 2026
Search Tags:#bioinformatics#genomics#sequence retrieval#variant analysis#ensembl#gene lookup
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-ensembl
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: db-ensembl
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-ensembl
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-ensembl

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 vast amounts of genomic data for over 250 species without manual database interaction.

Core Features & Use Cases

  • Gene Information: Retrieve details by symbol or ID.
  • Sequence Retrieval: Fetch DNA, transcript, or protein sequences.
  • Variant Analysis: Predict consequences using VEP.
  • Comparative Genomics: Find orthologs and paralogs.
  • Use Case: A researcher needs to find all human genes that are orthologous to a specific mouse gene and retrieve their protein sequences.

Quick Start

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

Frequently Asked Questions about db-ensembl

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve DNA or protein sequences from the Ensembl genome database?▼

Sequence retrieval from the Ensembl database is done by querying the REST API with a gene symbol or ID, allowing you to fetch specific DNA, transcript, or protein sequences across over 250 species.

How can I find orthologs for a specific gene across different species?▼

Finding orthologs across species uses the Ensembl REST API to perform comparative genomics queries, identifying orthologous and paralogous genes like finding mouse orthologs for the human BRCA2 gene.

Can I use the Ensembl REST API to predict variant consequences?▼

Variant analysis through the Ensembl REST API uses the VEP tool to predict consequences of genomic variants, integrating directly into research pipelines for efficient consequence assessment.

Does this Ensembl query method require the ensembl_rest Python package?▼

Querying Ensembl requires the ensembl_rest Python package and requests dependency, which provide the programmatic interface to access the REST API without manual database interaction.

What is the best way to automate genomic data retrieval for over 250 species?▼

Automating genomic data retrieval across 250 species uses the Ensembl REST API via Python scripts, enabling researchers to programmatically query gene information, sequences, and variants efficiently.

What are the limitations of using the Ensembl REST API for genomics research?▼

Limitations of the Ensembl REST API approach include potential query rate limits and dependency on REST endpoint availability, meaning it operates within the constraints of the remote database infrastructure.

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