IslandViewer 4

IslandViewer 4 predicts genomic islands in bacterial and archaeal genomes to identify clusters of horizontally transferred genes associated with virulence, antibiotic resistance, and other adaptive traits.

Key Features:

• Integrated prediction methods: Combines IslandPick (sequence composition bias), IslandPath-DIMOB (comparative genomics plus sequence composition), and SIGI-HMM (codon-usage HMM) for genomic island detection.
• Method-specific and overlapping predictions: Reports predictions from individual methods as well as overlapping/consensus genomic island calls.
• Custom genome analysis: Supports analysis of user-supplied genomic sequences for genomic island prediction.
• Annotation overlay: Maps annotations including virulence factors, antibiotic resistance genes, and pathogen-associated genes onto predicted genomic islands.
• Comparative genomic analysis: Provides comparative analysis of genomic islands between genomes.

Scientific Applications:

• Microbial pathogenesis: Identify genomic island-encoded virulence factors in bacteria and archaea.
• Antibiotic resistance: Detect antibiotic resistance genes located within genomic islands.
• Evolutionary biology: Study horizontal gene transfer and genomic adaptation in microbial evolution.
• Environmental and industrial microbiology: Investigate genes in genomic islands that contribute to environmental interactions and industrially relevant traits.

Methodology:

Prediction integrates IslandPick, IslandPath-DIMOB, and SIGI-HMM, combining sequence composition analysis, comparative genomics, and codon-usage HMMs to identify horizontally acquired gene clusters (genomic islands).