CGView pipeline

CGView specifications

Information


Unique identifier OMICS_00905
Name CGView
Alternative names Circular Genome Viewer, CGView Server
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Subtool


  • CGView Server

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Maintainers


  • person_outline Paul Stothard <>
  • person_outline Jason Grant <>

Additional information


Web app: http://stothard.afns.ualberta.ca/cgview_server/

Information


Unique identifier OMICS_00905
Name CGView
Alternative names Circular Genome Viewer, CGView Server
Interface Web user interface, Application programming interface
Restrictions to use None
Input data A DNA sequence.
Input format GenBank, EMBL, FASTA, or raw format.
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Subtool


  • CGView Server

Maintainers


  • person_outline Paul Stothard <>
  • person_outline Jason Grant <>

Additional information


Web app: http://stothard.afns.ualberta.ca/cgview_server/

Publications for Circular Genome Viewer

CGView IN pipelines

 (26)
2017
PMCID: 5282893
PMID: 28163825
DOI: 10.1186/s40793-017-0234-6

[…] with signal peptides883.89923.97934.16863.68genes with transmembrane helices58926.0660726.2060427.0058324.98crispr repeats30.0130.0130.0120.01 , a circular map was generated using the cgview web tool [20] that shows the relationship of the predicted proteins in the mb14, mb30, and mb66 genomes compared to strain mb11, in which the in silico assembly was corroborated by the optical […]

2017
PMCID: 5295034
PMID: 28106814
DOI: 10.3390/genes8010040

[…] (aic). mega6 [36] was used for the construction of the phylogenetic trees using the selected model., moreover, a gc skew analysis and an alignment of different phage genomes was performed using the cgview server [37]. the blast program used for this alignment was tblastx (translated dna vs. translated dna) [29,38]. finally, we used coregenes3.0 [39] for pairwise comparisons with the default […]

2017
PMCID: 5367828
PMID: 28346467
DOI: 10.1371/journal.pone.0174429

[…] [24]. the putative promoter upstream of the attachment site was predicted by bprom (http://www.softberry.com/berry.phtml). the circular map of the pa1 genome was generated using cgview (http://wishart.biology.ualberta.ca/cgview/) [25]. comparison of pp3-related cluster sequences was performed using brig (http://brig.sourceforge.net/) [26]., genomic dna was isolated […]

2017
PMCID: 5389983
PMID: 28450852
DOI: 10.3389/fmicb.2017.00573

[…] et al., 2014). the circular genome maps of the draft genome sequences of x. arboricola strains cita 14 and cita 124, representing the cog categories of the genes, were constructed using cgview (stothard and wishart, 2005). the contigs of both strains were arranged by mauve (darling et al., 2004, 2010) using the complete genome sequence of x. arboricola pv. juglandis xaj417 […]

2017
PMCID: 5707535
PMID: 29099783
DOI: 10.3390/v9110328

[…] sequences., phage draft genomes were visualized using blast ring image generator v0.95 (brig) [26]. alternatively, we ran a customized python script to produce xml files from blast results and used cgview java package to visualize them as circular genomes [27]., bins were classified into six categories according to high (ani ≥ 70%) or medium/low (ani < 70%) resemblance to a reference genome […]

CGView institution(s)
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada

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