skills.rest
CHENyiru3
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ensembl-database

Fetch gene annotations, sequences, variants, and orthologs via Ensembl REST API.

Updated Apr 19, 2026
Search Tags:#genomics#orthologs#rest-api#ensembl#variant-analysis#gene-lookup#sequence-retrieval
One-click install
npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill ensembl-database-chenyiru3
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ensembl-database
Source: https://github.com/CHENyiru3/AI-Skills-Collections/tree/main/skills-market/compbio/databases/ensembl
Command: npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill ensembl-database-chenyiru3

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Access Ensembl annotations, sequences, variants, and comparative genomics data programmatically via the REST API across 250+ species to accelerate genomic research workflows.

Core Features & Use Cases

  • Gene information: lookup by symbol or Ensembl ID to retrieve coordinates, transcripts, and cross-references.
  • Sequence retrieval: fetch genomic, transcript, and protein sequences for genes or regions.
  • Variant analysis: predict effects with VEP and obtain population and phenotype information.
  • Cross-species insights: find orthologs, paralogs, and perform comparative genomics analyses.

Quick Start

Use the Ensembl REST API to look up a human gene by symbol (e.g., BRCA2) and retrieve its gene info, sequence, and variant predictions in a single step.

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 annotations using the Ensembl REST API?▼

Use the Ensembl REST API to query gene annotations and sequences by inputting a gene symbol or Ensembl ID. This fetches genomic, transcript, and protein sequences alongside coordinates and cross-references for genomic research workflows.

Can I perform variant analysis and VEP predictions across multiple species?▼

Yes, you can perform variant analysis across 250+ species using the Ensembl REST API. It supports VEP predictions to determine variant effects and retrieves population and phenotype information for comparative genomics workflows.

What is the best way to find orthologs and paralogs for comparative genomics?▼

Finding orthologs and paralogs is achieved by querying Ensembl REST endpoints. This cross-species lookup retrieves comparative genomics data, enabling you to map homologous genes and perform comparative analysis across 250+ species.

Does querying the Ensembl REST API require specific error handling or rate limiting?▼

Querying the Ensembl REST API requires implementing rate limiting and error handling within your client environment. You must also maintain clear licensing awareness for data reuse when fetching gene and variant data programmatically.

How do I look up a human gene by symbol to get its coordinates and variant predictions?▼

Lookup a human gene by symbol, such as BRCA2, via the Ensembl REST API to retrieve its gene info, genomic sequence, and variant predictions in a single step. This returns coordinates, transcripts, and cross-references directly.

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