Ensembl Genomes Metazoa data slicer

Ensembl Genomes Metazoa data slicer extracts specified subsets of genomic data from BAM and VCF files and provides programmatic access to annotations, variants, regulatory features, and long-range interaction data across 87 metazoan species for comparative and variant analyses.

Key Features:

• Data Access Across Species: Supports access to genomic data from 87 species, including latest genome assemblies such as human, mouse, zebrafish, and rat, and maintains updates for previous assemblies like GRCh37 via dedicated platforms.
• BAM and VCF Slicing: Extracts specific genomic regions and subsets directly from BAM and VCF file formats.
• Integration of Third-Party Data: Incorporates additional third-party datasets into analyses to expand annotation and variant context.
• Scalable Analysis with REST: Provides RESTful APIs capable of handling large-scale genomic queries and programmatic access.
• Efficient Data Retrieval via BioMart: Uses BioMart for accelerated retrieval of regulatory and annotation data.
• Visualization of Long-Range Interactions: Supports display of long-range genomic interactions such as cis-regulatory contacts.

Scientific Applications:

• Genomic Annotation and Analysis: Facilitates detailed annotation and extraction of sequence features across multiple metazoan species.
• Comparative Genomics: Enables cross-species comparisons using consistent access to assemblies and annotations.
• Regulatory Network Exploration: Supports exploration of regulatory networks through retrieval and visualization of long-range interactions.
• Variant Analysis: Provides programmatic access to variant subsets for genetic variation studies and downstream analyses.

Methodology:

Slices specified regions from BAM and VCF files, integrates multiple datasets in a backend infrastructure, exposes scalable programmatic access via RESTful APIs, and retrieves regulatory annotations through BioMart.