Ensembl Genomes Plants sequence search

Ensembl Genomes Plants sequence search performs sequence similarity searches and comparative analyses across annotated plant genomes to identify homologous regions, genes, variants, and regulatory elements.

Key Features:

• Comprehensive Genome Access: Provides access to annotated plant genome assemblies and annotations, including newly added species.
• Sequence comparison with Exonerate: Uses Exonerate for precise sequence comparisons to identify homologous regions and functional elements.
• Integration with Ensembl infrastructure: Integrates Ensembl resources, including updated genome assemblies, annotations, and the Variant Effect Predictor (VEP) with additional third-party data.
• RESTful services for large-scale analyses: Supports scalable programmatic queries and large-scale analyses via RESTful services.
• Regulatory data retrieval via BioMart: Provides access to regulatory datasets and annotations through BioMart.
• Visualization of long-range interactions: Supports representation of long-range interactions, including cis-regulated datasets, for analysis of genetic regulation.

Scientific Applications:

• Genomic Annotation and Analysis: Annotating plant genomes and identifying genes and regulatory elements using annotated assemblies and sequence comparisons.
• Comparative Genomics: Comparing sequences across species to study evolutionary relationships and functional conservation.
• Functional Genomics: Investigating gene function and regulation through sequence comparison and variant annotation.
• Phenotypic Studies: Linking variant data to phenotypes to study genetic influences on plant traits.

Methodology:

Uses Exonerate for sequence comparison, leverages updated genome assemblies and annotations provided by Ensembl, and employs RESTful services for scalable programmatic access.