Creating a Genome Map

In order to create a GView map, only a sequence data file (for example a Genbank file) is needed, but GSS and GFF files may optionally be provided. Some example files are provided with GView in the downloads section, or in the GView Webstart section.

Once the appropriate files are obtained, there are are two different ways to use GView to create a genome map: using the GView Application, or using a Java program to access GView using the API. Most users will want to use the GView application, but the GView API can be used for integrating the GView Viewer into a larger application.

GView Application

screenshot-gview-application-small.png

GView is a complete program that can be executed on any computer with Java installed. The recommended method of using the GView application is in the interactive mode. In this mode, an interactive window with the genome map will be displayed. The map can be manipulated with the keyboard and mouse to explore the genome. Images of the view being displayed by GView can be captured and saved to a file.

GView can also be executed in a non-interactive mode that will create and save a single image of the genome map based on the parameters used on the command line. This mode is provided so that GView can be easily used by scripts.

GView can be deployed either online or as a standalone application.

GView API

The GView API allows interaction with GView through another Java application. This can be used to integrate the GView viewer into other applications for viewing genomes. More documentation and examples can be found in the GView API section, or within the GView application under the downloads section.
 
Contact: Aaron Petkau, Eric Marinier, Matthew Stuart-Edwards at gview@phac-aspc.gc.ca