ensembl-database

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

Updated Mar 10, 2026

Search Tags:#bioinformatics #genomics #orthologs #variant analysis #ensembl #gene lookup

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill ensembl-database-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/ensembl-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill ensembl-database-yezez9

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 needing to manually navigate complex web interfaces or download large datasets.

Core Features & Use Cases

Gene Information Retrieval: Look up genes by symbol or ID, retrieve sequences, and access cross-references.
Variant Analysis: Predict the functional consequences of genetic variants using the Variant Effect Predictor (VEP).
Comparative Genomics: Find orthologs and paralogs across different species to understand evolutionary relationships.
Use Case: A researcher needs to find all known variants associated with a specific gene (e.g., BRCA2) in humans and predict their potential impact on protein function.

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 query the Ensembl REST API for gene information and sequence retrieval?▼

Query the Ensembl REST API to look up genes by symbol or ID, retrieve genomic sequences, and access cross-references across 250+ species using the ensembl_rest Python package.

Can I find orthologs for a specific gene like BRCA2 in another species using Ensembl?▼

Find orthologs and paralogs across different species by querying the Ensembl database to understand evolutionary relationships, such as identifying orthologs for the human BRCA2 gene in mouse.

How do I predict the functional consequences of genetic variants using VEP?▼

Predict functional consequences of genetic variants using the Variant Effect Predictor (VEP) via the Ensembl REST API to analyze variant impacts on protein function.

What species are supported for comparative genomics through the Ensembl database?▼

Comparative genomics through the Ensembl database supports querying genomic data for over 250 species, enabling cross-species sequence retrieval and ortholog identification.

Do I need the ensembl_rest Python package to use this Ensembl API querying functionality?▼

You need the ensembl_rest Python package and the requests library to integrate Ensembl REST API querying capabilities into your genomic research pipelines and tools.