Can I retrieve protein sequences with this skill?

Yes, the skill can fetch protein, cDNA, and genomic DNA sequences in various formats including JSON, FASTA, and plain text.

Do I need to install any external Python packages?

While direct REST queries are possible via the 'requests' library, the 'ensembl_rest' Python package is recommended for a more Pythonic and efficient interface.

How does the skill handle Ensembl's API rate limits?

It follows best practices by respecting the 15 requests-per-second limit, handling 429 status codes with 'Retry-After' logic, and recommending batch endpoints for large queries.

Does this skill support the GRCh37 assembly?

Yes, the skill includes logic for querying both the current GRCh38 assembly and the legacy GRCh37/hg19 endpoints through specific host redirection.

Is there support for non-human species?

Yes, Ensembl provides comprehensive data for over 250 species including mouse, zebrafish, fruit fly, and many others, all accessible through this skill.

Ensembl Genome Database Access

Name: Ensembl Genome Database Access
Author: K-Dense-AI

byK-Dense-AI

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3,719

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Data Science & ML

Facilitates automated queries to the Ensembl REST API for gene annotation, sequence retrieval, and comparative genomic analysis across 250+ species.

This skill integrates the Ensembl genome database directly into Claude's environment, enabling researchers and developers to programmatically access high-quality vertebrate genomic data. It streamlines complex bioinformatics tasks such as mapping gene symbols to Ensembl IDs, retrieving DNA and protein sequences, predicting variant effects via VEP, and identifying cross-species orthologs. By automating interactions with the Ensembl REST API, it serves as a powerful bridge for genomic research pipelines, assembly mapping, and regulatory feature analysis, providing access to the latest biological data release (Release 115) and legacy assemblies like GRCh37.

Key Features

013,719 GitHub stars

02Genomic coordinate conversion between assemblies (e.g., GRCh37 to GRCh38)

03Variant Effect Predictor (VEP) integration for functional analysis

04Cross-species comparative genomics and orthology mapping

05Automated sequence retrieval for DNA, cDNA, and proteins

06Multi-species gene and transcript lookup by symbol or ID

Use Cases

01Analyzing clinical variants and predicting their functional consequences using VEP

02Building automated bioinformatics pipelines for gene annotation and sequence extraction

03Performing evolutionary studies by mapping orthologs and paralogs across vertebrate species

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills ensembl-database

For use in Claude.ai and ChatGPT

Download Skill