Circular genome visualization and exploration using CGView

By Paul Stothard, David S. Wishart. Bioinform., 2005

1,054 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/01a675819ea42c5bebef3519914b3eb2a06822af

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Citations in the corpus

DNAPlotter: circular and linear interactive genome visualization (2008, background): “CGView (Stothard and Wishart, 2005) is a circular genome viewer that produces PNG, JPEG or scalable vector graphics (SVG) format.”
ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes (2011, methodology): “…tab/ ’ Annotation Status ’ ), including a pie chart and histograms as well as a circular representation of the IS distribution using an integrated CGView tool [11] (Annotation tab/ ’ ISbrowser Preview ’ ) This is only accessible from a ‘ replicon page ’ , not from the ‘ project page ’ (see manual).”
BASys: a web server for automated bacterial genome annotation (2005, methodology): “For genome visualization and exploration, BASys relies heavily on the CGView application (19), a highly customizable circular genome rendering system that is well suited for use in bioinformatics pipelines.”
ggbio: an R package for extending the grammar of graphics for genomic data (2012, methodology): “There are many software packages that provide a circular overview plot, including Circos [10], CGView [23] and DNAplotter [24].”
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons (2011, methodology): “It uses CGView [16] for image rendering and BLAST [19] for genome comparisons.”
GenomeVx: simple web-based creation of editable circular chromosome maps (2008, background): “However, by making enquiries, we discovered that these maps are still often laboriously handdrawn, although there are at least three packages which can generate them (Gibson and Smith, 2003; Sato and Ehira, 2003; Stothard and Wishart, 2005).”
VFDB 2022: a general classification scheme for bacterial virulence factors (2021, background): “Since the database presents a dynamic circular map created by the CGView package (26) for each of the 32 genera, it offers an intuitive overview of the molecular diversity of bacterial VFs from various pathogens.”
Circos: an information aesthetic for comparative genomics. (2009, background): “Circularly arranged ideograms are prevalent in visualizations of microbial genomes, which are circular (Ghai and Chakraborty 2007; Gibson and Smith 2003; Kerkhoven et al. 2004; Pritchard et al. 2006; Sato and Ehira 2003; Stothard and Wishart 2005).”
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences (2012, background): “In terms of drawing circular chloroplast maps, several software packages and tools have been developed to suit this purpose [17-19].”
The CGView Server: a comparative genomics tool for circular genomes (2008, methodology): “The primary sequence file, BLAST results, GFF files and user options are passed to another Perl script, which builds an XML file for the CGView map-drawing program (8).”
Interactive microbial genome visualization with GView (2010, neutral): “CGView (Stothard and Wishart, 2005) and Circos (Krzywinski et al., 2009) can generate very high quality, highly customizable circular maps in bitmap and scalable vector graphics (SVG) formats, and can be incorporated in pipelines, but have limited interactivity, and like their predecessors, require…”
OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes (2007, methodology): “More specialized tools (e.g., CGView: Stothard and Wishart 2005; Tsudzuki 2000) can produce decent maps of some organellar genome sequences, but oVer little convenience and Xexibility and, moreover, require special input Wle formats that must be generated manually.”
Comparing thousands of circular genomes using the CGView Comparison Tool (2012, methodology): “CCT consists of several custom Bash and Perl scripts that are used to create a local COG sequence database [4], download sequences of interest from NCBI [5], extract and translate ORFs, extract CDS feature translations, perform BLAST searches [6], assign COG functional categories to proteins, genera”