Do I need a specific Python package to use this skill?

While you can use standard HTTP libraries like 'requests', this skill recommends and provides examples for the 'ensembl_rest' Python package.

Does this skill handle API rate limiting for Ensembl?

Yes, it provides best practices for respecting Ensembl's limit of 15 requests per second, including handling 429 status codes and using batch endpoints.

What type of sequence data can I retrieve?

You can fetch genomic DNA sequences, transcript sequences (cDNA), and protein sequences, with options for flanking regions.

Which species does the Ensembl Database skill support?

It supports over 250 species, including humans (Homo sapiens), mice (Mus musculus), zebrafish (Danio rerio), and fruit flies (Drosophila melanogaster).

Can I use this skill to convert GRCh37 coordinates to GRCh38?

Yes, the skill includes specialized support and implementation patterns for assembly mapping between different genome versions.

Ensembl Genome Database

Name: Ensembl Genome Database
Author: pur3v4d3r

bypur3v4d3r

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Data Science & ML

Queries the Ensembl REST API to retrieve gene annotations, sequences, variants, and comparative genomic data for over 250 species.

About

This skill empowers researchers and bioinformaticians to programmatically access the Ensembl genome database, a premier resource for vertebrate genomic data maintained by EMBL-EBI. It facilitates automated gene lookups, sequence extraction (DNA, cDNA, and protein), and sophisticated variant analysis using the Variant Effect Predictor (VEP). Whether performing comparative genomics to find orthologs or mapping coordinates between genome assemblies like GRCh37 and GRCh38, this skill provides the patterns and best practices needed to streamline complex genomic workflows directly within a Claude-powered development environment.

Key Features

Sequence Retrieval: Extract genomic, transcript, and protein sequences in JSON, FASTA, or plain text.
Variant Effect Prediction: Analyze genetic variants and predict functional consequences using VEP.
Gene & Transcript Lookup: Search by symbol, Ensembl ID, or external identifiers across 250+ species.
Comparative Genomics: Identify orthologs, paralogs, and evolutionary gene trees across species.
1 GitHub stars
Assembly Mapping: Convert coordinates between different genome versions, such as GRCh37 to GRCh38.

Use Cases

Predicting the functional impact and population frequency of clinical genetic variants.
Automating gene annotation and sequence extraction pipelines for genomic research projects.
Conducting cross-species evolutionary analysis to identify conserved genetic elements and orthologs.

About

Key Features

Sequence Retrieval: Extract genomic, transcript, and protein sequences in JSON, FASTA, or plain text.
Variant Effect Prediction: Analyze genetic variants and predict functional consequences using VEP.
Gene & Transcript Lookup: Search by symbol, Ensembl ID, or external identifiers across 250+ species.
Comparative Genomics: Identify orthologs, paralogs, and evolutionary gene trees across species.
1 GitHub stars
Assembly Mapping: Convert coordinates between different genome versions, such as GRCh37 to GRCh38.

Use Cases

Predicting the functional impact and population frequency of clinical genetic variants.
Automating gene annotation and sequence extraction pipelines for genomic research projects.
Conducting cross-species evolutionary analysis to identify conserved genetic elements and orthologs.