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

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Ressource 1Download: Bertelli2017NAR_IslandViewer4.pdf (695.99 [Ko])
State: Public
Version: Final published version
Serval ID
serval:BIB_D8A6D1AB7FE1
Type
Article: article from journal or magazin.
Publication sub-type
Review (review): journal as complete as possible of one specific subject, written based on exhaustive analyses from published work.
Collection
Publications
Title
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
Journal
Nucleic acids research
Author(s)
Bertelli C., Laird M.R., Williams K.P., Lau B.Y., Hoad G., Winsor G.L., Brinkman FSL
Working group(s)
Simon Fraser University Research Computing Group
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
03/07/2017
Peer-reviewed
Oui
Volume
45
Number
W1
Pages
W30-W35
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
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.

Pubmed
Web of science
Open Access
Yes
Create date
12/01/2018 11:21
Last modification date
20/08/2019 15:58
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