Genome Maps

Genome Maps visualizes genomic features and large-scale next-generation sequencing datasets to enable exploration and interpretation of genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms (SNPs), karyotypes, and associated Variant Call Format (VCF) and Binary Alignment/Map (BAM) files via annotations from web services and Distributed Annotation System (DAS) servers.

Key Features:

• HTML5 and SVG rendering: Uses HTML5 web standards and scalable vector graphics (SVG) to provide optimized server-side and client-side rendering and efficient data transfer.
• Data management model: Employs a novel data handling model that optimizes workloads and supports scalability for increasing genomic datasets from next-generation sequencing.
• Comprehensive biological representation: Supports visualization of genes, transcripts, exons, regulatory features, SNPs, karyotypes, and other annotation types imported from web services and presented as tracks.
• DAS integration: Includes support for Distributed Annotation System (DAS) servers to access external genomic annotations.
• Local VCF and BAM handling: Supports local upload and client-side visualization of large VCF and BAM files for real-time rendering and management of potentially sensitive medical data.

Scientific Applications:

• Genomics research: Exploration and interpretation of complex genomic datasets derived from next-generation sequencing.
• Variant analysis and clinical genomics: Inspection and visualization of VCF and BAM files to support variant interpretation and handling of sensitive medical data.
• Annotation aggregation: Integration of annotations from web services and DAS servers for comparative annotation and functional context.

Methodology:

Implements HTML5 and SVG-based rendering, a client-server data management model optimized for workload distribution, imports annotations from web services and DAS servers, and supports client-side parsing and visualization of VCF and BAM files.