Which programming languages work best with this skill?

This skill is optimized for Python, providing implementation patterns for both the ensembl_rest library and direct HTTP requests using the requests package.

Does this skill support the GRCh37 (hg19) assembly?

Yes, the skill includes specific instructions and endpoints for querying the GRCh37 archive and mapping coordinates to the current GRCh38 assembly.

What kind of variant analysis can I perform?

You can look up variants by rsID, retrieve population frequency data, and use the Variant Effect Predictor (VEP) to determine functional consequences.

Can I perform batch queries for multiple genes or variants?

Yes, the skill provides guidance on using Ensembl's batch endpoints to efficiently handle multiple lookups while respecting API rate limits.

Ensembl Genome Database Integration

Name: Ensembl Genome Database Integration
Author: Sologa

bySologa

0•

データサイエンスとML

Simplifies access to the Ensembl REST API for comprehensive genomic data retrieval, sequence analysis, and variant prediction across 250+ species.

The Ensembl Database skill empowers Claude to interact directly with the Ensembl REST API, providing a powerful toolkit for genomic research and bioinformatics. It facilitates seamless gene annotation lookups, DNA and protein sequence retrieval, and advanced comparative genomics. By leveraging the latest Ensembl releases, researchers can perform variant effect predictions (VEP), identify orthologs across species, and map coordinates between genome assemblies like GRCh37 and GRCh38. This skill is essential for automating biological data pipelines, analyzing genetic variations, and integrating high-quality vertebrate genomic data into research workflows.

主な機能

01Genomic coordinate mapping and liftover between different assembly versions

020 GitHub stars

03Cross-species comparative genomics to identify orthologs and paralogs

04Comprehensive gene annotation lookups by symbol, Ensembl ID, or external identifiers

05High-speed sequence retrieval for DNA, transcripts, and proteins in multiple formats

06Automated Variant Effect Predictor (VEP) for predicting functional consequences

ユースケース

01Analyzing genetic variants to predict functional impacts on protein-coding regions

02Automating gene annotation and sequence extraction for large-scale genomic studies

03Performing evolutionary analysis by identifying orthologs across vertebrate species

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline ensembl-database

For use in Claude.ai and ChatGPT

Download Skill