IslandViewer 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


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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

 (12)
2017
PMCID: 5604767
PMID: 28818894
DOI: 10.1128/genomeA.00771-17

[…] automatic annotation pipeline (pgaap) (7). additionally, the genomes were analyzed on the rapid annotation using subsystems technology (rast) server (8). genome island detection was achieved using islandviewer 4 (9). acquired antibiotic resistance genes were identified using resfinder 2.1 (10), virulence factors using virulencefinder 1.2 (11), clustered regularly interspaced short palindromic […]

2016
PMCID: 4971109
PMID: 27536275
DOI: 10.3389/fmicb.2016.01180

[…] on the genomic blast dendrogram. as a result, a collection of 26 genome sequences was used for pangenome analysis (figure s1). for each strain, horizontally transferred genes were identified by islandviewer (dhillon et al., 2015) and detailed information of horizontally transferred genes identified for all strains were summarized into table s2. we obtained rna-seq data for 4 e. coli strains […]

2015
PMCID: 4535895
PMID: 26484173
DOI: 10.1016/j.gdata.2015.01.006

[…] 30–84 and o6 was conducted using the img website's tool, which defined genes with a 60% identity at an e-value < 10− 2 as homologous to those in ht66. the genomic islands were identified using islandviewer (http://www.pathogenomics.sfu.ca/islandviewer/query.php) [20]. secondary metabolite production clusters were examined using the antismash program […]

2015
PMCID: 4665904
PMID: 26629309
DOI: 10.1186/s40793-015-0109-7

[…] further investigation.fig. 4, for other features of the genome, 612 tandem repeats were found in the genome by tandem repeats finder [30]. there are at least 58 genomic islands being predicted by islandviewer [31]. on-line crisprfinder [32] has identified ten crispr regions with one confirmed and nine questionable crisprs. four incomplete and one questionable prophage regions were identified […]

2014
PMCID: 3924358
PMID: 24526626
DOI: 10.1128/genomeA.00009-14

[…] islands (gis) are clusters of genes in prokaryotic genomes of probable horizontal origin and are often associated with microbial adaptations of medical or environmental interest (18). using the islandviewer software (19), we predicted 6 putative gis in the genome of f. nucleatum w1481. an examination of the gis revealed the presence of genes involved in clustered regularly interspaced short […]

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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