IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis

Area of Science:

• Microbial genomics
• Bioinformatics
• Genomic island analysis

Background:

• Genomic islands (GIs) are crucial for microbial adaptation, often encoding antimicrobial resistance and virulence factors.
• IslandViewer is a popular web resource for identifying GIs in bacterial and archaeal genomes.

Purpose of the Study:

• To introduce IslandViewer 3, a major update to the IslandViewer web resource.
• To enhance genomic island analysis and visualization capabilities for microbial genomes.

Main Methods:

• Development of IslandPlot, an interactive genome visualization tool with synchronized views.
• Incorporation of curated virulence factors and antimicrobial resistance genes, with homolog identification.
• Recalculation of pathogen-associated genes and improved handling of incomplete genomes.

Main Results:

• IslandViewer 3 provides interactive genome analysis and gene search functionalities.
• The updated resource includes more curated medically relevant genes and their homologs.
• The system now supports analysis of incomplete microbial genomes and features an improved queuing system.

Conclusions:

• IslandViewer 3 represents a significant advancement in genomic island analysis software.
• New features enhance its utility for broader microbial genome analysis and visualization.
• The tool is valuable for studying microbial adaptations, including antimicrobial resistance and virulence.