Does this skill support the legacy GRCh37 assembly?

Yes, it supports both the current GRCh38 assembly and the legacy GRCh37/hg19 assembly by utilizing the specific grch37.rest.ensembl.org endpoints.

Does it require specific Python packages?

While it can use standard HTTP libraries like 'requests', it recommends the 'ensembl_rest' Python package for a more idiomatic and efficient development experience.

Can I retrieve protein sequences directly using this skill?

Yes, the skill provides methods to fetch protein sequences based on Ensembl IDs, symbols, or specific genomic regions in various formats.

Can I use this for non-vertebrate species?

While Ensembl focuses on vertebrates, the skill provides access to all species supported by the Ensembl REST API, currently totaling over 250.

What is the best way to handle Ensembl API rate limits?

The skill recommends respecting the 15 requests per second limit, handling 429 status codes by checking 'Retry-After' headers, and using batch endpoints for multi-item queries.

Ensembl Genomic Database Integration

Name: Ensembl Genomic Database Integration
Author: x-cmd

byx-cmd

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Data Science & ML

Accesses and analyzes comprehensive vertebrate genomic data from the Ensembl REST API for over 250 species.

About

This skill provides a robust interface for Claude to interact with the Ensembl genome database, a premier resource for vertebrate genomic data maintained by EMBL-EBI. It enables automated gene annotation, sequence retrieval (DNA, cDNA, and protein), variant effect prediction using VEP, and comparative genomics across a vast range of species. It is particularly useful for bioinformatics researchers and developers building genomic data pipelines who need reliable, real-time access to the latest assembly information, evolutionary data, and cross-database references.

Key Features

8 GitHub stars
DNA, cDNA, and protein sequence retrieval in multiple formats including FASTA
Cross-species comparative genomics including ortholog and paralog identification
Coordinate mapping and conversion between genome assemblies like GRCh37 and GRCh38
Comprehensive gene and transcript annotation lookups by symbol or ID
Variant Effect Predictor (VEP) integration for functional consequence analysis

Use Cases

Predicting the functional consequences of genetic variants for clinical or research studies
Building automated bioinformatics pipelines for gene annotation and sequence analysis
Conducting evolutionary studies by mapping orthologs and paralogs across hundreds of vertebrate species

About

Key Features

8 GitHub stars
DNA, cDNA, and protein sequence retrieval in multiple formats including FASTA
Cross-species comparative genomics including ortholog and paralog identification
Coordinate mapping and conversion between genome assemblies like GRCh37 and GRCh38
Comprehensive gene and transcript annotation lookups by symbol or ID
Variant Effect Predictor (VEP) integration for functional consequence analysis

Use Cases

Predicting the functional consequences of genetic variants for clinical or research studies
Building automated bioinformatics pipelines for gene annotation and sequence analysis
Conducting evolutionary studies by mapping orthologs and paralogs across hundreds of vertebrate species