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Nucleic Acids Research Advance Access originally published online on April 14, 2008
Nucleic Acids Research 2008 36(Web Server issue):W181-W184; doi:10.1093/nar/gkn179
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W181-W184
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

The CGView Server: a comparative genomics tool for circular genomes

Jason R. Grant and Paul Stothard*

Department of Agricultural, Food and Nutritional Science, University of Alberta, Canada T6G 2P5

*To whom correspondence should be addressed. Tel: +1 780 492 5242; Fax: +1 780 492 9234; Email: stothard{at}ualberta.ca

Received January 28, 2008. Revised March 17, 2008. Accepted March 28, 2008.

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/


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