GeCoViz

GeCoViz visualizes genomic contexts surrounding prokaryotic genes to support functional and evolutionary analysis.

Key Features:

• Reference genomes database: Contains 12,221 reference prokaryotic genomes used for analyses and visualizations.
• Search capabilities: Supports queries by gene names, orthologous groups (KEGGs and eggNOGs), protein domains (PFAM), or direct sequence input.
• Scaled genomic visualizations: Renders dynamic plots with scaled depictions of gene lengths and genomic distances.
• Synteny conservation analysis: Performs on-the-fly calculations of synteny conservation among neighboring genes and highlights genes based on custom-defined thresholds.
• Taxonomic scope customization: Allows adjustment of taxonomic scope for comparative analyses across species.
• Neighboring gene annotations: Provides detailed annotations for neighboring genes to enrich contextual interpretation.
• High-resolution output export: Produces plots that can be exported as high-resolution images.

Scientific Applications:

• Synteny conservation analysis: Infers potential functional roles of unknown prokaryotic genes by identifying conserved genomic neighborhoods.
• Gene function and comparative genomics: Enables comparative analyses of gene neighborhoods to investigate gene function across diverse species.
• Evolutionary biology: Supports studies of gene neighborhood evolution and broader evolutionary relationships among prokaryotes.

Methodology:

Uses a database of 12,221 reference prokaryotic genomes, supports searches by gene identifiers (gene names, KEGG, eggNOG), PFAM domains, or sequence input, renders scaled gene-length and genomic-distance visualizations, and performs on-the-fly calculations of synteny conservation with customizable thresholds.