ensembl-database

What problem does it solve?

Accessing and integrating diverse genomic data from the Ensembl database can be complex and time-consuming, hindering rapid genomic research. This Skill streamlines queries for genes, sequences, variants, and comparative genomics, accelerating your analysis and reducing manual data wrangling.

Core Features & Use Cases

• Gene & Sequence Retrieval: Look up gene information by symbol or Ensembl ID, and fetch DNA, transcript, or protein sequences for over 250 species.
• Variant Analysis: Query genetic variation data and predict functional consequences of variants using the Variant Effect Predictor (VEP).
• Comparative Genomics: Easily find orthologs (same gene in different species) and paralogs (related genes in the same species) to understand evolutionary relationships.
• Use Case: A geneticist needs to find all orthologs of a human gene (e.g., BRCA2) in mice, retrieve their protein sequences, and analyze any known variants. This skill automates the entire data retrieval and initial analysis, providing a comprehensive overview.

Quick Start

To look up a human gene by symbol: from ensembl_rest import EnsemblClient client = EnsemblClient() gene_data = client.symbol_lookup(species='human', symbol='BRCA2') print(gene_data)