ensembl-database
Ensembl Genome Database
Overview
Ensembl is a comprehensive genome annotation database covering 300+ vertebrate and non-vertebrate species. The Ensembl REST API provides programmatic access to gene models, transcript/protein sequences, variant annotations, cross-references, regulatory features, and comparative genomics without requiring any login or API key.
When to Use
- Retrieving official gene and transcript annotations (stable IDs, biotype, genomic coordinates) for human or model organism genes
- Converting between gene identifier namespaces (HGNC symbol ↔ Ensembl ID ↔ RefSeq ↔ UniProt)
- Fetching genomic or cDNA/CDS/protein sequences for a gene or transcript
- Looking up variant consequences and functional impact (VEP) for a list of SNPs
- Querying regulatory features (promoters, enhancers, CTCF sites) in a genomic region
- Performing comparative genomics queries (orthologs, paralogs, gene trees) across species
- For local offline access to large genomic annotations, use
pyensemblinstead - For pathway and metabolic annotations, use
kegg-databaseorreactome-databaseinstead
Prerequisites
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