Ensembl Genomes Bacteria sequence search

Ensembl Genomes Bacteria sequence search performs sequence searches and alignments in the Ensembl Bacteria database using Exonerate to support comparative analyses and annotation of bacterial genomes.

Key Features:

• Exonerate integration: Uses Exonerate for sequence comparison and alignment to identify homologous regions among bacterial genomes.
• Ensembl Bacteria data: Operates on Ensembl Bacteria genome assemblies and annotations covering 87 species across main and early access releases.
• Variant Effect Predictor (VEP) interoperability: Integrates with VEP enhancements that incorporate additional third-party data for variant annotation.
• REST API support: Interacts with the Ensembl REST API to enable larger-scale programmatic analyses.
• BioMart compatibility: Leverages BioMart for retrieval of regulatory and genomic data with improved performance.

Scientific Applications:

• Genetic variation identification: Detects and aligns sequences to identify genetic variants across bacterial genomes.
• Comparative genomics: Identifies homologous regions and supports genome-to-genome comparisons among bacteria.
• Evolutionary analysis: Enables analyses of sequence conservation and divergence for evolutionary studies.
• Functional annotation: Supports annotation of bacterial genes and genomic features using Ensembl assemblies and VEP data.
• Pathogenesis and antibiotic resistance research: Facilitates investigation of genomic determinants of pathogenesis and antibiotic resistance mechanisms.

Methodology:

Performs sequence alignment and comparison using Exonerate within the Ensembl Bacteria database and utilizes Ensembl genome assemblies and annotations together with Variant Effect Predictor (VEP), the Ensembl REST API, and BioMart for analysis and data retrieval.