Can I retrieve protein sequences for non-human species?

Yes, the Ensembl skill supports data retrieval for over 250 species, including common model organisms like mouse, zebrafish, and fruit flies.

How does the skill handle Ensembl API rate limits?

It implements API best practices by respecting the 15 requests per second limit and providing patterns to handle 429 status codes using the Retry-After header.

What is the recommended way to use this skill in Python?

The recommended approach is to install the 'ensembl_rest' Python package, though it also supports direct REST API calls using standard HTTP libraries like requests.

Does this skill support the GRCh37 (hg19) assembly?

Yes, the skill includes logic to query the GRCh37-specific REST endpoint and supports coordinate mapping between GRCh37 and GRCh38.

Ensembl Genome Database

Name: Ensembl Genome Database
Author: Microck

byMicrock

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Data Science & ML

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

About

This skill provides Claude with specialized capabilities to interact with the Ensembl genome database, a premier resource for vertebrate genomic data maintained by EMBL-EBI. It streamlines bioinformatics workflows by enabling direct lookups of gene symbols, retrieval of transcript and protein sequences, variant effect predictions (VEP), and comparative genomics analysis across 250+ species. It is particularly useful for researchers and bioinformaticians who need to integrate real-time genomic data, cross-reference external databases, or perform cross-species orthology mapping within their development environment.

Key Features

Map genomic coordinates between different assemblies like GRCh37 and GRCh38
Query gene information and chromosomal coordinates by symbol or Ensembl ID
Retrieve DNA, cDNA, and protein sequences in JSON, FASTA, or plain text
Identify orthologs and paralogs for comparative evolutionary studies
81 GitHub stars
Predict functional consequences of genetic variants using VEP analysis

Use Cases

Automating gene annotation pipelines for large-scale genomic research
Performing cross-species comparisons to identify conserved evolutionary sequences
Analyzing clinical variants to predict functional impacts and population frequencies

About

Key Features

Map genomic coordinates between different assemblies like GRCh37 and GRCh38
Query gene information and chromosomal coordinates by symbol or Ensembl ID
Retrieve DNA, cDNA, and protein sequences in JSON, FASTA, or plain text
Identify orthologs and paralogs for comparative evolutionary studies
81 GitHub stars
Predict functional consequences of genetic variants using VEP analysis

Use Cases

Automating gene annotation pipelines for large-scale genomic research
Performing cross-species comparisons to identify conserved evolutionary sequences
Analyzing clinical variants to predict functional impacts and population frequencies