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

Abstract

IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization.

Figure 1.

IslandViewer 3 results page for Salmonella enterica subsp. enterica serovar Typhi str. Ty2 (accession number NC_004631.1). Panel (A) is the circular genome view, panel (B) is the vertical view with text descriptions of genes and gene products and panel (C) is the horizontal view to enable users to zoom in/out of regions of interest. Within each panel, GI predictions are represented as blocks (integrated results in red, IslandPick in green, SIGI-HMM in orange and IslandPath-DIMOB in blue), virulence genes (purple for curated, light purple for homologs), antimicrobial resistance genes (pink for curated, light pink for homologs) and pathogen-associated genes (orange) as circular glyphs. The legend can be used to turn individual items on/off in the circular view. Users can click on any island or double-click on any other region of panel (A), which will then zoom-in to those regions in panels (B) and (C) for more details. New in the toolbox, users can now search for a particular gene of interest and save a customized view.