cgview - 0.0.20100111-7 main

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