Ensembl Genomes Plants assembly converter

Ensembl Genomes Plants Assembly Converter maps plant genomic data onto current genome assemblies to enable up-to-date comparative and variant analyses and access to regulatory and long-range interaction datasets.

Key Features:

• Alignment with current assemblies: Maps user-provided plant genomic data onto the most recent genome assemblies to maintain coordinate and annotation consistency.
• Integration with Ensembl resources: Operates within the Ensembl framework and integrates data from Ensembl main and early access platforms.
• Support for multiple species: Supports plant genomes across the Ensembl Genomes Plants collection, including the stated set of 87 species.
• Variant Effect Predictor (VEP) and BioMart integration: Integrates with VEP and BioMart, incorporating additional third-party datasets and improved performance for variant annotation and data retrieval.
• Regulatory data and long-range interactions: Provides access to regulatory datasets and enables viewing of long-range interactions within cis-regulated datasets.
• Programmatic large-scale analysis: Exposes RESTful APIs for large-scale programmatic analysis and data access.
• Third-party dataset integration: Incorporates third-party datasets into mapping and annotation workflows to enhance analytical context.

Scientific Applications:

• Comparative genomics: Enable comparative genomic studies using standardized coordinates on the latest assembly versions.
• Variant effect analysis: Support annotation and interpretation of genetic variation effects using VEP integration.
• Regulatory and interaction analysis: Facilitate analysis of regulatory elements and long-range cis interactions relevant to gene expression and regulation in plants.
• Large-scale data retrieval and analysis: Support bulk retrieval and programmatic analyses of plant genomic data via BioMart and RESTful APIs.

Methodology:

Maps plant genomic data onto current assemblies within the Ensembl framework, uses RESTful APIs for large-scale analysis, employs BioMart for data retrieval, and integrates third-party datasets for annotation.