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.
Highlights
Genomic islands (GIs) are commonly defined as clusters of genes of probable horizontal origin >8 kb in size in bacterial and archaeal genomes [1]
Many virulence factor and/or antimicrobial resistance genes are shared and acquired via GIs [4] and genes such as virulence factors have been shown to be disproportionately associated with these GI regions [5]
It should be noted that while there are limitations to GI analysis of such draft or incomplete genomes, reasonable results can be obtained for genomes with few contigs that aligned to a highly similar reference genome such as from a closely related strain
Summary
Genomic islands (GIs) are commonly defined as clusters of genes of probable horizontal origin >8 kb in size in bacterial and archaeal genomes [1]. In previous versions of IslandViewer, a basic circular genome visualizer has allowed users to view GIs, with links to a table providing annotations of the genes in the predicted GI regions.
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