IslandViewer update: Improved genomic island discovery and visualization.

Bhavjinder K. Dhillon, Terry A. Chiu, Matthew R. Laird, Morgan G.I. Langille, Fiona S.L. Brinkman

Research output: Contribution to journalArticlepeer-review

80 Citations (Scopus)

Abstract

IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a web-accessible application for the computational 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 because they disproportionately encode virulence factors and other adaptations of medical, environmental and industrial interest. Many computational tools exist for the prediction of GIs, but three of the most accurate methods are available in integrated form via IslandViewer: IslandPath-DIMOB, SIGI-HMM and IslandPick. IslandViewer GI predictions are precomputed for all complete microbial genomes from National Center for Biotechnology Information, with an option to upload other genomes and/or perform customized analyses using different settings. Here, we report recent changes to the IslandViewer framework that have vastly improved its efficiency in handling an increasing number of users, plus better facilitate custom genome analyses. Users may also now overlay additional annotations such as virulence factors, antibiotic resistance genes and pathogen-associated genes on top of current GI predictions. Comparisons of GIs between user-selected genomes are now facilitated through a highly requested side-by-side viewer. IslandViewer improvements aim to provide a more flexible interface, coupled with additional highly relevant annotation information, to aid analysis of GIs in diverse microbial species.

Original languageEnglish
Pages (from-to)W129-132
JournalUnknown Journal
Volume41
Issue numberWeb Server issue
DOIs
Publication statusPublished - Jul 2013

Bibliographical note

Funding Information:
Genome British Columbia/Genome Canada; the Simon Fraser University Community Trust Endowment Fund; Canadian Institutes for Health Research Bioinformatics Training Program scholarship (to B.K.D.); Canadian Institute for Health Research (Postdoctoral Fellowship Award to M.G.I.L.); the Michael Smith Foundation for Health Research (Scholar Award to F.S.L.B.). Funding for open access charge: Genome Canada.

ASJC Scopus Subject Areas

  • Genetics

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