Also provided is a well-documented API (application program interface), which allows the CGView Java code to be used in other applications. Simpler input formats are supported, which allow the positions of genes to be described, but which offer less control over how the information is displayed. The contents of a sample XML file and the resulting map generated by CGView are shown in Figure 1. The SVG format offers advantages for image editing and printing, but the file size can be problematic when complex maps are generated. Bitmap images (PNG or JPG) or vector-based output in SVG (Scalable Vector Graphics) format can be generated. CGView supports a custom XML (Extensible Markup Language) input format for describing the contents and appearance of a map, which the program then converts into graphical format.
Originally intended for bacterial genomes, it has proven to be popular for organellar genomes as well. The Circular Genome ViewerĬGView ( ) is a Java program developed in 2005 as a tool for generating high-quality, navigable maps of circular genomes. Our focus in this review is on bacterial genome visualization software, specifically on the Circular Genome Viewer (CGView) family of visualization tools. These tools lack many of the capabilities of full-genome browsers but can be used to quickly generate visually appealing and compact circular maps that are often used in publications to highlight specific findings of interest or to convey summary information. Recent examples include Circleator, CiVi and SynTView. However, given the relatively small size and in most cases circular topology of bacterial chromosomes, a variety of bacterial-specific visualization tools have been developed. Genome browsers like Ensembl, IGV and JBrowse offer an impressive array of features including interfaces for searching and map customization, and can be applied to eukaryotic and prokaryotic genomes. Numerous genome visualization tools exist. Further feature types of potential value include the positions of sequence differences with respect to a closely related genome, gene expression information at the level of transcription or protein abundance, the positions of contig boundaries for incomplete genomes and sequence coverage information. For example, including a GC content graph and BLAST comparison results may reveal that key components of the pathway were likely acquired through horizontal gene transfer. Additional information relating to specific positions of the sequence can be displayed to further aid in interpretation. For example, on a map that displays the positions of genes, the judicious use of color and text can highlight gene families or functions of interest, to indicate that a genome has the capacity to produce the components of a particular pathway. Genome maps can effectively convey information that can aid in understanding the biological properties and evolutionary history of organisms. Genome visualization, genome analysis, bacteria, organelles Introduction