Is it possible to find orthologs between different species?

Yes, the Comparative Genomics feature allows you to find orthologs and paralogs, and even retrieve gene trees showing evolutionary relationships.

Can I retrieve protein sequences for specific gene transcripts?

Absolutely. The skill covers fetching genomic, transcript (cDNA), and protein sequences in various formats including JSON and FASTA.

Can I use this for bulk genomic data queries?

Yes, it provides implementation patterns for using batch endpoints and handling Ensembl's specific rate limiting (15 requests per second) to ensure high-volume queries succeed.

Does this skill support the GRCh37 (hg19) assembly?

Yes, the skill includes specific instructions and endpoints for querying the GRCh37 archive as well as the most current genome assemblies like GRCh38.

What Python libraries are required for this skill?

The skill recommends the 'ensembl_rest' package for a Pythonic interface, but it also provides examples using the standard 'requests' library for direct API calls.

Ensembl Genome Database

Name: Ensembl Genome Database
Author: Microck

byMicrock

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Data Science & ML

Queries the Ensembl REST API to retrieve gene annotations, sequences, variants, and comparative genomics data for over 250 species.

This skill provides specialized knowledge and implementation patterns for interfacing with the Ensembl genome database, a premier resource maintained by EMBL-EBI. It enables researchers to programmatically perform gene lookups, fetch DNA and protein sequences, analyze genetic variants with the Variant Effect Predictor (VEP), and identify orthologs across species. By incorporating best practices for rate limiting, batch processing, and coordinate mapping (e.g., GRCh37 to GRCh38), this skill empowers developers to build robust bioinformatics pipelines and automated genomic research tools directly within the Claude environment.

Key Features

01Gene information retrieval by symbol, ID, or external cross-references

02High-speed DNA, transcript (cDNA), and protein sequence fetching

0381 GitHub stars

04Comparative genomics tools for finding orthologs and paralogs

05Assembly mapping and coordinate conversion between genome releases

06Variant Effect Predictor (VEP) integration for functional analysis

Use Cases

01Analyzing genetic variants to predict clinical or functional consequences

02Conducting cross-species evolutionary studies and gene tree analysis

03Automating genomic annotation pipelines for large-scale research projects

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills ensembl-database

For use in Claude.ai and ChatGPT

Download Skill