IslandViewer protocols

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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


Add your version

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 in pipelines

 (36)
2018
PMCID: 5754498
PMID: 29301889
DOI: 10.1128/genomeA.01419-17

[…] of the uv4 and uv4/95 draft genomes with p. putida f1 using mauve () revealed the absence of a 90-kb-long region in uv4 and f1 compared to uv4/95, which was later identified as a genomic island by islandviewer (). the genomic island contains 88 genes, the majority of which are of unknown function or related to phage proteins., a detailed functional annotation of protein-coding genes […]

2018
PMCID: 5793183
PMID: 29324691
DOI: 10.3390/genes9010031

[…] was generated using the cgview comparison tool []. island viewer was used to identify chromosomal deviations in gc content, known as genomic islands (geis) (http://www.pathogenomics.sfu.ca/islandviewer/) []. the genome, with a coverage of 90x, was then annotated and genes predicted by img/er [], rast [], and national center for biotechnology information’s (ncbi) prokaryotic genomes […]

2018
PMCID: 5817063
PMID: 29491851
DOI: 10.3389/fmicb.2018.00184

[…] a wgmlst tree with p. agglomerans pc10 and p. stewartii subsp. indologens lmg 2632 selected as outgroups (accession nz_lime00000000.1 and jpko00000000.1). genomic islands were identified using the islandpath dimob function on islandviewer4 server (bertelli et al., ). partial and complete phage regions were identified in the genome assemblies of the wgs strains using phaster. circular genome […]

2018
PMCID: 5851621
PMID: 29538430
DOI: 10.1371/journal.pone.0194088

[…] .0 [], basic local alignment search tool (blast®, []), pseudomonas genome database (www.pseudomonas.com, []), antibiotics & secondary metabolite analysis shell (antismash) v. 3.0.5 [] and the islandviewer 3 software []. synteny analyses were performed with the simplesynteny platform (https://www.dveltri.com/simplesynteny/index.html, [])., all draft and complete assemblies, and protein […]

2018
PMCID: 5908935
PMID: 29674546
DOI: 10.1128/genomeA.00277-18

[…] 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 b […]


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IslandViewer in publications

 (246)
PMCID: 5908935
PMID: 29674546
DOI: 10.1128/genomeA.00277-18

[…] 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 b […]

PMCID: 5930311
PMID: 29500259
DOI: 10.1128/AEM.02828-17

[…] 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 […]

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

[…] 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 […]

PMCID: 5880901
PMID: 29636744
DOI: 10.3389/fmicb.2018.00577

[…] the number of independent combinations., insertion sequences (is) and transposases distributed over l. ferriphilum 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 […]

PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069

[…] with prokka (seemann ) using a custom protein database built from the pseudomonas genus. the annotations were then searched for prophages using phaster (arndt et al.), and genomic islands using the islandviewer and antismash (bertelli et al.; blin et al.). for the latter, the reference genome used for the alignment was that of p. koreensis strain d26 as it was deemed phylogenetically close […]


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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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