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Protocols

IslandViewer specifications

Information


Unique identifier OMICS_08266
Name IslandViewer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

Subtools


  • Islander
  • IslandPath-DIMOB
  • IslandPick
  • SIGI-HMM

Versioning


No version available

Maintainer


  • person_outline Fiona S.L. Brinkman

Information


Unique identifier OMICS_08266
Name IslandViewer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 4.0
Stability Stable
Maintained Yes

Subtools


  • Islander
  • IslandPath-DIMOB
  • IslandPick
  • SIGI-HMM

Maintainer


  • person_outline Fiona S.L. Brinkman

Publications for IslandViewer

IslandViewer citations

 (289)
call_split

Complete Genome Sequence of Shewanella sp. WE21, a Rare Isolate with Multiple Novel Large Genomic Islands

2018
Genome Announc
PMCID: 5908935
PMID: 29674546
DOI: 10.1128/genomeA.00277-18
call_split See protocol

[…] version 2.1 (), virulence factors by using VirulenceFinder version 1.2 (), clustered regularly interspaced short palindromic repeat (CRISPR) arrays by using CRISPRFinder (), genomic islands by using IslandViewer version 4 (), and prophage-related sequences by using PHASTER ().The final assembly for Shewanella sp. strain WE21 resulted in one large closed contig with a total length of 5,266,746 bp […]

library_books

Background Adjusted Alignment Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

2018
Front Microbiol
PMCID: 5911508
PMID: 29713314
DOI: 10.3389/fmicb.2018.00711

[…] ased on this data set and the resulting figures are shown in Figure . It is clear from the figure that CVT(3), d2*(3,1) and d2*(4,1) perform much better than the other methods. In Langille et al. (), SIGI-HMM and IslandPath/DIMOB showed the highest accuracy of 0.86. We did not include them in our comparison because they incorporate other information such as codon uasge, dinucleotide bias, gene exp […]

library_books

Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes

2018
Appl Environ Microbiol
PMCID: 5930311
PMID: 29500259
DOI: 10.1128/AEM.02828-17

[…] osa SCV20265 and 70.8% in S. cinnamoneus) versus the genome averages (66.3% and 72.4%, respectively), the clusters were not predicted to be part of genomic islands in these strains when analyzed with IslandViewer4 ().However, analysis of the genomic context of bcm gene clusters in P. aeruginosa strains strongly supports an insertion hypothesis, since the genes that flank the cluster are contiguous […]

library_books

Draft Genome Sequence of Bacillus paralicheniformis F47, Isolated from an Algerian Salty Lake

2018
Genome Announc
PMCID: 5876485
PMID: 29599156
DOI: 10.1128/genomeA.00190-18

[…] (GGDC) 2.1 server (). Secondary metabolites were predicted using antiSMASH v4 (), and bacteriocins were predicted using BAGEL4 (http://bagel4.molgenrug.nl) (). Genomic islands were predicted by using IslandViewer 4.0 (), prophages by using PHASTER (), and clustered regularly interspaced short palindromic repeats (CRISPRs) by using CRISPRfinder ().Genome annotation by the NCBI PGAP predicted 4,117 […]

library_books

Pan Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation

2018
Front Microbiol
PMCID: 5880901
PMID: 29636744
DOI: 10.3389/fmicb.2018.00577

[…] rriphilum genomes were predicted and classified using the ISFinder platform (). A developed IslandViewer 3 (), which integrates two sequence composition genomic islands (GIs) prediction method, i.e., IslandPath-DIMOB () and SIGI-HMM (), and a comparative genomic GIs prediction method IslandPick (), was applied for the computational identification of putative GIs. In addition, CRISPR (Clustered Reg […]

library_books

Community led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies

2018
FEMS Microbiol Lett
PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069

[…] ary of the antiSMASH results is provided in (Grant, Arantes and Stothard ). Many of the loci referred to throughout this manuscript are labelled around the CCT map in Fig.  as well as the results of IslandViewer. The CCT BLAST analysis confirms the close phylogenetic relationship between P. baetica a390 and Irchel 3E19 (Fig. ). Of the nine biosynthetic gene clusters (BGCs) predicted by antiSMASH, […]

Citations

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IslandViewer institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; Systems Biology Department, Sandia National Laboratories, Livermore, CA, USA; Big Data Hub, Simon Fraser University, Burnaby, BC, Canada
IslandViewer funding source(s)
Supported by Swiss National Science Foundation fellowship [P300- PA 164673]; Societé Académique Vaudoise, Genome Canada, Genome BC; Cystic Fibrosis Foundation; and the Laboratory Directed Research and Development program at Sandia National Laboratories.

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