Can I retrieve protein sequences with this skill?

Absolutely. You can fetch protein, cDNA, and genomic DNA sequences using Ensembl IDs or genomic coordinates.

Can I find orthologs for a human gene in other species?

Yes, the comparative genomics capability allows you to identify orthologs and paralogs across more than 250 species supported by Ensembl.

How does the skill handle Ensembl API rate limits?

It includes best practices for respecting the 15 requests per second limit, handling 429 status codes, and implementing retry logic with the Retry-After header.

Is the ensembl_rest Python package required?

While the ensembl_rest package is recommended for a cleaner Pythonic interface, the skill also provides patterns for making direct HTTP requests using standard libraries like 'requests'.

Does this skill support the human genome GRCh37 (hg19)?

Yes, the skill provides specific instructions and endpoints for querying legacy GRCh37 data as well as the current GRCh38 assembly.

Ensembl Genome Database Integration

Name: Ensembl Genome Database Integration
Author: ricable

byricable

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Data Science & ML

Accesses the Ensembl REST API to retrieve genomic sequences, gene annotations, and variant data for over 250 species.

The Ensembl Database skill empowers researchers and bioinformaticians to programmatically interact with the EMBL-EBI Ensembl genome database directly through Claude. It provides a robust interface for querying gene information by symbol or ID, fetching DNA and protein sequences, performing variant effect predictions (VEP), and conducting comparative genomics across hundreds of species. This skill is essential for automating genomic research pipelines, identifying orthologs, and integrating high-quality biological data directly into AI-driven scientific workflows, ensuring efficient data retrieval with built-in best practices for rate limiting and assembly mapping.

Key Features

01Gene information retrieval by symbol, Ensembl ID, or external identifiers

02High-fidelity genomic, transcript, and protein sequence fetching in JSON/FASTA

031 GitHub stars

04Comparative genomics tools to identify cross-species orthologs and paralogs

05Variant Effect Predictor (VEP) integration for functional consequence analysis

06Coordinate mapping and conversion between genome assemblies (e.g., GRCh37 to GRCh38)

Use Cases

01Automating gene annotation and sequence retrieval pipelines for genomic research

02Conducting large-scale evolutionary studies through cross-species comparative analysis

03Analyzing genetic variants to predict phenotypic consequences and population frequencies

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ricable/ultimate-ai-agent ensembl-database

For use in Claude.ai and ChatGPT

Download Skill