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. 2017 Jul 3;45(W1):W30-W35.
doi: 10.1093/nar/gkx343.

IslandViewer 4: Expanded Prediction of Genomic Islands for Larger-Scale Datasets

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Free PMC article

IslandViewer 4: Expanded Prediction of Genomic Islands for Larger-Scale Datasets

Claire Bertelli et al. Nucleic Acids Res. .
Free PMC article

Abstract

IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.

Figures

Figure 1.
Figure 1.
Example IslandViewer 4 results. Predictions of genomic islands in the Salmonella enterica str. Ty2 genome (accession number NC_004631.1). Circular (A) and linear (B) visualization of predicted genomic islands are shown, with blocks colored according to the prediction method; IslandPick (green), IslandPath-DIMOB (blue), SIGI-HMM (orange), Islander (turquoise) as well as the integrated results (dark red). Virulence genes (purple for curated, light purple for homologs), antimicrobial resistance genes (pink for curated, light pink for homologs) and pathogen-associated genes (yellow) are also visible as circular glyphs. Tickboxes in the legend enable users to turn on/off individual items in the circular view. Double clicking on any region zooms into the region in panel (B) and opens a vertical view of the genes and their description (C) within the region selected in the circular view. Circular or horizontal views can be exported to obtain publication-grade customized figures.

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