IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

TLDR

IslandViewer is a widely‑used webserver that predicts and visualizes genomic islands—regions of probable horizontal origin—in bacterial and archaeal genomes, which often encode virulence factors and other adaptations that enhance microbial competitiveness. The authors release IslandViewer 4, adding features to support larger‑scale microbial genomics, expanding GI predictions, and improving its flexible visualization interface. IslandViewer 4 introduces a user‑management web interface and a secured HTTP API for batch analyses, and enhances integrated GI predictions by incorporating the precise Islander method for pre‑computed genomes and an updated IslandPath‑DIMOB for both pre‑computed and custom genomes. Pre‑computed predictions—including virulence factors and antimicrobial resistance—are now available for 6,193 complete bacterial and archaeal strains in RefSeq, enabling better analysis of GIs and insight into their role in the evolution of environmental microbes and pathogens.

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.