Which species are supported by the Ensembl Database skill?

The skill supports over 250 species, including human (Homo sapiens), mouse (Mus musculus), zebrafish (Danio rerio), and fruit fly (Drosophila melanogaster).

Can I use this skill to map coordinates between different genome versions?

Yes, the skill includes assembly mapping capabilities, allowing you to convert genomic coordinates between versions like GRCh37 (hg19) and GRCh38.

Can I retrieve protein sequences for specific gene transcripts?

Absolutely. You can look up a gene, identify its transcripts, and retrieve the corresponding protein sequences in various formats like JSON or FASTA.

Does this skill handle Ensembl REST API rate limiting?

Yes, the skill provides implementation patterns for handling 429 status codes, respecting the 'Retry-After' header, and utilizing batch endpoints to stay within the 15 requests per second limit.

Ensembl Genome Database Integration

Name: Ensembl Genome Database Integration
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Queries the Ensembl REST API for genomic data, sequence retrieval, variant analysis, and comparative genomics across 250+ species.

This skill provides a comprehensive interface for Claude to interact with the Ensembl genome database, a premier resource for vertebrate genomic data maintained by EMBL-EBI. It enables automated retrieval of gene annotations, DNA/protein sequences, and evolutionary relationships (orthologs/paralogs) directly within the development environment. Bioinformaticians and researchers can use this skill to streamline genomic pipelines, perform variant effect predictions (VEP), and map coordinates between genome assemblies, significantly reducing the manual effort required for biological data gathering.

Key Features

01Gene and transcript lookup by symbol, Ensembl ID, or external identifiers

02Genomic assembly mapping for converting coordinates between GRCh37 and GRCh38

03Variant Effect Predictor (VEP) integration for functional consequence analysis

04High-throughput sequence retrieval for DNA, cDNA, and protein sequences

05Comparative genomics tools to identify orthologs and paralogs across species

060 GitHub stars

Use Cases

01Analyzing functional consequences of genetic variants using VEP predictions

02Conducting cross-species evolutionary studies by identifying orthologous gene sets

03Automating gene annotation and sequence fetching for bioinformatics pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos ensembl-database

For use in Claude.ai and ChatGPT

Download Skill