The CGView Server: a comparative genomics tool for circular genomes

By Jason R. Grant, Paul Stothard. Nucleic Acids Res., 2008

1,316 citations recorded by the source corpus.

The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature or analysis information can be submitted in the form of GFF (General Feature Format) files. The server uses BLAST to compare the primary sequence to up to three comparison genomes or sequence sets. The BLAST results and feature information are converted to a graphical map showing the entire sequence, or an expanded and more detailed view of a region of interest. Several options are included to control which types of features are displayed and how the features are drawn. The CGView Server can be used to visualize features associated with any bacterial, plasmid, chloroplast or mitochondrial genome, and can aid in the identification of conserved genome segments, instances of horizontal gene transfer, and differences in gene copy number. Because a collection of sequences can be used in place of a comparison genome, maps can also be used to visualize regions of a known genome covered by newly obtained sequence reads. The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/

Subfields: Molecular Biology, Plant Science

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Citations in the corpus

Pseudomonas simiae WCS417: star track of a model beneficial rhizobacterium (2020, methodology): “The circular diagram is prepared with CGView (Grant and Stothard 2008) Genomes of Pseudomonas spp. typically contain gene clusters for five of the six identified bacterial protein secretion systems (type I, II, III, V and VI).”
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements (2018, methodology): “ICEfinder uses the CGView circular genome visualization tool (23) to display the distribution of the predicted T4SS-type ICEs, IMEs and AICEs in the query bacterial genome.”
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons (2011, methodology): “BRIG DNAPlotter [12] CGView Server[13] GeneWiz Browser[14] Microbial Genome Viewer[10] Genome Projector[11]”
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing (2015, methodology): “Comparison of experimental mitochondrial DNA to published mitochondrial DNA (NCBI accession GQ162109) was performed using the CGView Server with the default options [101].”
Comparing thousands of circular genomes using the CGView Comparison Tool (2012, methodology): “For bacterial genomes, we previously created the CGView Server [8], which can compare a reference genome to up to three comparison genomes, using nucleotide or translated nucleotide BLAST searches.”
OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets (2013, background): “CGView (17) provides a more flexible framework for creating circular genome maps, and the CGView server also has a web browser interface.”