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GView specifications

Information


Unique identifier OMICS_13423
Name GView
Alternative name GView Server
Interface Web user interface
Restrictions to use None
Output format PNG, JPG, SVG
Programming languages Java
License GNU Affero General Public License version 3
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Gary Van Domselaar <>

Information


Unique identifier OMICS_13423
Name GView
Alternative name GView Server
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Output format PNG, JPG, SVG
Operating system Unix/Linux
Programming languages Java
License GNU Affero General Public License version 3
Computer skills Medium
Version 1.7
Stability Stable
Source code URL https://www.gview.ca/files/release/1.7/gview-1.7-src.zip
Maintained Yes

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Documentation


Maintainer


  • person_outline Gary Van Domselaar <>

Publications for GView

GView in pipelines

 (7)
2018
PMCID: 5867892
PMID: 29558450
DOI: 10.3390/genes9030171

[…] these were complete or draft sequences of the l. monocytogenes genome (). the genome sequences were downloaded from the genbank database., a comparative analysis of the genome content using gview [] generated a pangenome profile of the l. monocytogenes isolates. the pangenome was constructed by iteratively appending unique regions onto an initial seed genome. genbank files for three […]

2017
PMCID: 5237526
PMID: 28088165
DOI: 10.1186/s12864-016-3447-y

[…] core genus level were subtracted from each core species genome., for each one of the 4 compared ensifer species, a pan-genome analysis was also performed using blast analyzes as implemented in the gview package [] with as cutoffs, 1e-10 e-value, 80% identity and 80% of minimal alignment length., to get insights in functions associated to desert symbiotic bacteria, clusters of orthologous […]

2017
PMCID: 5720691
PMID: 29216329
DOI: 10.1371/journal.pone.0189319

[…] frames (orfs) of fv113-g1 as queries against draft-genome sequences of strains atcc 8501t and atcc 27725, atcc 49185 and 12-1b, respectively (), followed by visualizing the search results with gview server (https://server.gview.ca/) []., phylogeny was generated using the maximum-likelihood phylogenetic method with fasttree v2.1.10 []., orthology analysis was performed using orthovenn […]

2016
PMCID: 4707298
PMID: 26793180
DOI: 10.3389/fmicb.2015.01547

[…] to facilitate visualization on the extensive diversity of the 18 studied incfiia plasmids, circular maps displaying the core and accessory genomes of all the studied plasmids were visualized using gview server (petkau et al., ), with plasmid pec302/04 assigned as the seed genome. ta systems for all plasmids genomes were identified as described in section plasmid gap closing and annotation., […]

2015
PMCID: 4278250
PMID: 25552925
DOI: 10.7150/ijbs.10320

[…] respectively. insertion sequences were predicted by using is finder. nucleotide sequence was compared against the nucleotide collection database in ncbi using blastn. figure was generated using gview server. mauve2.3.1 was used to perform comparative plasmid genome alignment. figure was drawn using genomediagram, . orthologous groups of genes from pkf3-140, pip1206 and dh10b […]


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GView in publications

 (39)
PMCID: 5867892
PMID: 29558450
DOI: 10.3390/genes9030171

[…] fine snp analysis are summarized in ., the pan-genome for 38 isolates, including 25 clinical isolates, six food/food processing environment isolates and seven reference genomes, was generated using gview []. approximately 85% of the coding sequences consist of mutually conserved core genes as shown in . this analysis demonstrates that a significant proportion of the l. monocytogenes genome […]

PMCID: 5827749
PMID: 29483539
DOI: 10.1038/s41598-018-21919-4

[…] through idba-ud algorithm centred on de bruijn graph approach. genome annotation was carried out using the ncbi ‘prokaryotic genome annotation pipeline’. genomic context was visualized through gview. prophage regions were identified using phast and antibiotic resistance was profiled through blast module of ardb. resistance gene identifier (rgi) listed at card site […]

PMCID: 5820359
PMID: 29503635
DOI: 10.3389/fmicb.2018.00220

[…] to delineate species boundaries as it correlates well to dna-dna hybridization studies (goris et al., ; federhen et al., )., comparative genomic and gene cluster analyses were performed using the gview tools (petkau et al., ) and proteinortho (lechner et al., ), respectively. the comparisons involved the bacterial strain panel. in proteinortho, co-orthologous clustering was calculated using […]

PMCID: 5749857
PMID: 29293692
DOI: 10.1371/journal.pone.0190836

[…] 90% identity or greater, 1556 (76.4%) are present at 80% identity or greater, and 1589 (80.1%) are present at 70% identity or greater. this corresponds to the extensive core genome identified using gview server [,] ( and ). in contrast, the accessory genome of isolates 00–0949 and 01–1512 is more extensive than isolates 00–6200 and 00–1597, and appears to be almost identical in both 00–0949 […]

PMCID: 5720691
PMID: 29216329
DOI: 10.1371/journal.pone.0189319

[…] frames (orfs) of fv113-g1 as queries against draft-genome sequences of strains atcc 8501t and atcc 27725, atcc 49185 and 12-1b, respectively (), followed by visualizing the search results with gview server (https://server.gview.ca/) []., phylogeny was generated using the maximum-likelihood phylogenetic method with fasttree v2.1.10 []., orthology analysis was performed using orthovenn […]


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GView institution(s)
National Microbiology Laboratory – Public Health Agency of Canada, Winnipeg, MB, Canada; Department of Computer Science, University of Manitoba, Canada; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
GView funding source(s)
Supported by Canada’s National Microbiology Laboratory.

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