ensembl-database

Topics in the source

• Ensembl Database
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Gene Information Retrieval
• 2. Sequence Retrieval
• 3. Variant Analysis
• 4. Comparative Genomics

Access and query the Ensembl genome database, a comprehensive resource for vertebrate genomic data maintained by EMBL-EBI. The database provides gene annotations, sequences, variants, regulatory information, and comparative genomics data for over 250 species. Current release is 115 (September 2025). This skill should be used when: Querying gene information by symbol or Ensembl ID Retrieving DNA, transcript, or protein sequences Analyzing genetic variants using the Variant Effect Predictor (VEP) Finding orthologs and paralogs across species Accessing regulatory features and genomic annotations Converting coordinates between genome assemblies (e.g., GRCh37 to GRCh38) Performing comparative genomics analyses Integrating Ensembl data into genomic research pipelines Query gene data by symbol, Ensembl ID, or external database identifiers. Common operations: Look up gene information by symbol (e.g., "BRCA2", "TP53") Retrieve transcript and protein information Get gene coordinates and chromosomal locations Access cross-references to external databases (UniProt, RefSeq, etc.) Using the ensemblrest package: Direct REST API (no package): Fetch genomic, transcript, or protein sequences in vari

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