cgview

Circular Genome Viewer

Description

CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases.

In addition to the CGView application, an API is available for generating maps from within other Java applications, using the cgview package.

CGView can be used for any of the following:

* Bacterial genome visualization and browsing - CGView can be

incorporated into bacterial genome annotation pipelines, as a means

of generating web content for data visualization and navigation. The

PNG and image map content does not require Java applets or special

browser plugins.

* Genome poster generation - CGView can generate poster-sized images of

circular genomes in rasterized image formats or in Scalable Vector

Graphics format.

* Sequence analysis visualization - CGView can be used to display the

output of sequence analysis programs in a circular context.

CGView features:

* Images can be generated in PNG, JPG, or SVG format. See the

CGView gallery.

* Static or interactive maps can be generated. The interactive maps

make use of standard PNG images and HTML image maps. Scalable Vector

Graphics output is included in the interactive maps (see example).

* The XML input allows complete control over the appearance of the map.

* Tab delimited input files and NCBI ptt files can be used as an

alternative to the XML format.

* The CGView API can be used to incorporate CGView into Java

applications.

* The CGView applet can be used to incorporate zoomable maps into web

pages (see example).

* The CGView Server can be used to generate maps online.

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Homepage

http://wishart.biology.ualberta.ca/cgview/

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