Can this skill handle coordinate mapping between genome versions?

Yes, it provides specific implementations for assembly mapping, allowing you to convert coordinates between different versions like GRCh37 (hg19) and GRCh38.

What formats are supported for sequence retrieval?

The skill demonstrates how to fetch sequences in multiple formats, including JSON for programmatic processing and FASTA or plain text for standard bioinformatics workflows.

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

The skill includes best practices and code patterns for respecting Ensembl's 15 requests per second limit, including logic for handling 429 status codes and the 'Retry-After' header.

Which species are supported by this Ensembl skill?

The skill supports over 250 species available in the Ensembl database, including humans (Homo sapiens), mice (Mus musculus), and other key vertebrates and model organisms.

Does it support the Variant Effect Predictor (VEP)?

Yes, one of the core capabilities is querying the VEP through the REST API to predict the functional consequences of variants using HGVS notation or genomic coordinates.

Ensembl Genome Database Access

Name: Ensembl Genome Database Access
Author: Activer007

byActiver007

0•

数据科学与机器学习

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

This skill empowers Claude to interact directly with the Ensembl genome database, a premier resource for vertebrate genomics maintained by EMBL-EBI. It facilitates complex bioinformatics tasks such as gene ID mapping, sequence retrieval (DNA, cDNA, protein), variant consequence prediction via VEP, and cross-species comparative analysis. Whether you are building genomic research pipelines or performing ad-hoc data lookups, this skill provides the necessary patterns and best practices for efficient, rate-limit-aware API communication across multiple genome assemblies.

主要功能

01Comprehensive gene lookup by symbol, Ensembl ID, or external identifiers

02High-fidelity sequence retrieval for DNA, transcripts, and proteins

03Genetic variant analysis and functional consequence prediction via VEP

04Automated coordinate conversion between genome assemblies (e.g., GRCh37 to GRCh38)

050 GitHub stars

06Comparative genomics tools to identify orthologs and paralogs

使用场景

01Analyzing the functional impact of genetic variants in clinical or population studies

02Performing cross-species evolutionary analysis to identify conserved genomic features

03Automating gene annotation and sequence retrieval pipelines for bioinformatics research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills ensembl-database

For use in Claude.ai and ChatGPT

Download Skill