OpenGenomeBrowser

OpenGenomeBrowser organizes and analyzes genomic datasets to support comparative genomics, phylogenetics, and functional genomics investigations across bacterial, archaeal, and yeast genomes.

Key Features:

• Phylogenetic tree generation: Generates phylogenetic trees from genomic data.
• Gene loci comparison: Compares gene loci across genomes to identify conserved and variable regions.
• Biochemical pathway browsing: Enables browsing and inspection of biochemical pathways associated with genomic features.
• BLAST searches: Performs BLAST searches against hosted genomic datasets.
• Data visualization: Produces dot plots and other visual representations for comparative genomic analyses.
• Gene trait matching: Performs gene trait matching to identify functional associations within and across genomes.
• Modular data organization: Uses a modular folder structure to organize genomic data and metadata and to streamline analysis automation.
• User management: Implements user management for controlled access and collaborative research.

Scientific Applications:

• Comparative genomics: Supports genome-to-genome comparisons across bacterial, archaeal, and yeast genomes.
• Phylogenetics: Facilitates phylogenetic analyses through tree reconstruction and comparative metrics.
• Functional genomics: Enables gene-trait matching and pathway-level investigations to link genes to functions.

Methodology:

Implements database-independent management of genomic datasets and a modular folder structure to automate analyses, and provides computational methods explicitly including phylogenetic tree generation, gene loci comparison, BLAST searches, biochemical pathway browsing, dot plot generation, and gene-trait matching.