Visualizing and comparing circular genomes using the CGView family of tools

• Published in: Briefings in bioinformatics Vol. 20; no. 4; pp. 1576 - 1582
• Main Authors: Stothard, Paul, Grant, Jason R, Van Domselaar, Gary
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 19.07.2019; Oxford Publishing Limited (England)
• Subjects: Chromosome Mapping; Computational Biology; Computer Graphics; DNA, Circular - genetics; Escherichia coli O157 - genetics; Gene mapping; Genome, Bacterial; Genome, Viral; Genomes; Genomics - statistics & numerical data; Graphical user interface; Listeria monocytogenes - genetics; Nucleotide sequence; Organelles; Software; Software Review; User-Computer Interface; genome visualization; bacteria; organelles; genome analysis
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbx081

Abstract Graphical genome maps are widely used to assess genome features and sequence characteristics. The CGView (Circular Genome Viewer) software family is a popular collection of tools for generating genome maps for bacteria, organelles and viruses. In this review, we describe the capabilities of the original CGView program along with those of subsequent companion applications, including the CGView Server and the CGView Comparison Tool. We also discuss GView, a graphical user interface-enabled rewrite of CGView, and the GView Server, which offers several integrated analyses for identifying shared or unique genome regions relative to a collection of comparison genomes. We conclude with some remarks about our current development efforts related to CGView aimed at adding new functionality while increasing ease of use.