What sequence formats are supported?

You can retrieve sequences in multiple formats including JSON, FASTA, and plain text for genomic regions, transcripts, and proteins.

Is a Python environment required to use this skill?

While the ensembl_rest Python package is recommended for a cleaner interface, the skill also supports direct HTTP requests to the REST API.

How do I find orthologs between humans and other species?

The skill uses homology endpoints to identify orthologs (same gene in different species) and paralogs (related genes in the same species).

Does it support batch queries to avoid rate limits?

The skill includes best practices for handling rate limits, including the use of batch endpoints and managing 429 status codes with retry logic.

Can I use this skill for the GRCh37 (hg19) human assembly?

Yes, the skill provides specific instructions and endpoints for accessing the legacy GRCh37 assembly alongside the current GRCh38 release.

Ensembl Genome Database

Name: Ensembl Genome Database
Author: BbgnsurfTech

byBbgnsurfTech

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データサイエンスとML

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

概要

The Ensembl Genome Database skill provides a powerful interface for Claude to interact with the EMBL-EBI Ensembl genomic resource. It enables researchers and developers to perform complex genomic queries including gene symbol lookups, sequence retrieval (DNA, cDNA, and protein), and functional variant analysis via the Variant Effect Predictor (VEP). With support for over 250 species and comparative genomics capabilities, this skill is essential for identifying orthologs, analyzing evolutionary relationships, and mapping coordinates between genome assemblies like GRCh37 and GRCh38 within automated research pipelines.

主な機能

Gene information lookup by symbol, Ensembl ID, or external identifiers
High-throughput sequence retrieval for DNA, transcripts, and proteins
3 GitHub stars
Genomic assembly mapping and coordinate conversion (e.g., Liftover)
Variant consequence prediction and population frequency analysis using VEP
Comparative genomics tools for identifying orthologs and paralogs

ユースケース

Automating gene annotation and sequence extraction for bioinformatics pipelines
Predicting the functional impact of genetic variants in clinical research datasets
Conducting cross-species evolutionary analysis to identify conserved genomic regions

概要

主な機能

Gene information lookup by symbol, Ensembl ID, or external identifiers
High-throughput sequence retrieval for DNA, transcripts, and proteins
3 GitHub stars
Genomic assembly mapping and coordinate conversion (e.g., Liftover)
Variant consequence prediction and population frequency analysis using VEP
Comparative genomics tools for identifying orthologs and paralogs

ユースケース

Automating gene annotation and sequence extraction for bioinformatics pipelines
Predicting the functional impact of genetic variants in clinical research datasets
Conducting cross-species evolutionary analysis to identify conserved genomic regions