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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数据科学与机器学习

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

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.

主要功能

018 GitHub stars

02DNA, cDNA, and protein sequence retrieval in multiple formats including FASTA

03Cross-species comparative genomics including ortholog and paralog identification

04Coordinate mapping and conversion between genome assemblies like GRCh37 and GRCh38

05Comprehensive gene and transcript annotation lookups by symbol or ID

06Variant Effect Predictor (VEP) integration for functional consequence analysis

使用场景

01Predicting the functional consequences of genetic variants for clinical or research studies

02Building automated bioinformatics pipelines for gene annotation and sequence analysis

03Conducting evolutionary studies by mapping orthologs and paralogs across hundreds of vertebrate species

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add x-cmd/skill ensembl-database

For use in Claude.ai and ChatGPT

Download Skill