ensembl-database

Name: ensembl-database
Availability: InStock
Author: rubensliv

Query Ensembl REST API data for genes, sequences, variants, and comparative genomics.

15|2|Updated Dec 17, 2025

Search Tags:#genomics #orthologs #sequence #rest-api #ensembl #assembly-mapping #variant-analysis

Ready to run

npx skills add https://github.com/rubensliv/k-dense-ai --skill ensembl-database-rubensliv

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/ensembl-database
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill ensembl-database-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Researchers need programmatic access to Ensembl's genomic resources to automate querying genes, sequences, variants, and comparative data across hundreds of species. This skill provides a unified client and workflow for retrieving gene annotations, DNA/protein sequences, variant effects, and cross-species analyses, enabling reproducible genomic research pipelines.

Core Features & Use Cases

Gene lookup by symbol or Ensembl ID to fetch coordinates, transcripts, and cross-references
Sequence retrieval for genomic, transcript, and protein sequences
Variant analysis with VEP predictions and population data
Comparative genomics with orthologs, paralogs, and gene trees
Assembly mapping and coordinate conversion between GRCh37 and GRCh38
Region-based overlap queries to discover features in genomic intervals

Quick Start

Query Ensembl for a gene's details, sequences, and variant predictions to begin a genomic analysis.

Frequently Asked Questions about ensembl-database

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 REST API?▼

Yes, you can retrieve sequences from the Ensembl REST API by querying endpoints for genomic, transcript, or protein sequences using an Ensembl ID. This process returns raw sequence data for downstream genomic research pipelines.

Can I map genomic coordinates between GRCh37 and GRCh38 assemblies?▼

You can map genomic coordinates between GRCh37 and GRCh38 assemblies using assembly mapping endpoints. This action converts coordinate positions across different reference assemblies for accurate cross-species comparisons and variant analysis.

What is the best way to find orthologs and paralogs for a gene across 250+ species?▼

Finding orthologs and paralogs across 250+ species involves querying comparative genomics endpoints. Querying gene trees and homology data returns cross-species comparative results for evolutionary analysis.

Does this Ensembl API client handle rate limiting and errors automatically?▼

The Ensembl API client handles rate limiting and errors automatically through its robust Python implementation. It manages request throttling and error handling to ensure reliable data retrieval during genomic queries.

How do I run VEP predictions for variant analysis using Ensembl data?▼

Running VEP predictions for variant analysis involves querying specific Ensembl REST API endpoints with variant identifiers. This action returns predicted variant effects and population data for genomic research.

Do I need the requests library to query Ensembl data across species?▼

You need the requests library installed to query Ensembl data across species. The Python client depends on it to execute REST API calls for gene lookup, sequence retrieval, and comparative genomics.