Ensembl Genomes Protists sequence search

Ensembl Genomes Protists sequence search performs sequence alignment and retrieval across protist genomes using Exonerate to support genome annotation, comparative genomics, and functional analyses.

Key Features:

• Integration with Exonerate: Uses Exonerate to perform sequence alignment and comparison to identify homologous sequences across protist genomes.
• Access to extensive genomic data: Provides access to Ensembl comprehensive genomic datasets including newly annotated protists and updates across species including human, mouse, zebrafish, and rat.
• Enhanced analytical tools (VEP integration): Integrates Variant Effect Predictor (VEP) with additional third-party data sources to expand variant annotation capabilities.
• Scalability and programmatic access: Exposes RESTful services for large-scale analyses and BioMart for rapid retrieval of regulatory data.
• Visualization of long-range interactions: Supports visualization of long-range genomic interactions and cis-regulated datasets for regulatory analysis.

Scientific Applications:

• Genome annotation: Facilitates annotation of protist genomes to identify genes, regulatory elements, and genomic features.
• Comparative genomics: Enables cross-species comparisons to investigate evolutionary relationships and functional conservation.
• Functional genomics: Supports identification of gene function through sequence homology and variant effect annotation.
• Regulatory network analysis: Aids analysis of gene regulation by integrating long-range interaction visualizations and regulatory datasets.

Methodology:

Sequence alignments are performed using Exonerate and analyses leverage Ensembl comprehensive databases and analytical tools; the system integrates third-party data sources, exposes RESTful services for scalability, and uses BioMart for rapid regulatory data access.