Chromoscape is a java applet-based application which can be used to view and manipulate graphical depictions of genomic mapping data. Chromoscape runs in association with an Internet browser on a user's machine, and no installation is necessary.

Chromoscape is used here to graphically view genomic data from eGenome. The process of creating and using a graphical view consists of several steps:

1. Specifying the region to be viewed
2. Loading the graphic onto the user's browser
3. Customizing the graphic for optimal viewing
4. Analyzing the data displayed in the graphic

On this page, each of the steps will be explained briefly to get the user started. More detailed information and explanation of advanced features are covered in subsequent sections.

To begin the process of viewing a region with Chromoscape, the user must define the region of interest. The most precise way of defining a region is by using the search for a region console and selecting the view results as a graphic option. Help for specifying a region for viewing can be found here. Viewing a whole chromosome in Chromoscape, available with the view whole chromosome console, can also be performed in a simpler process. Help for viewing a whole chromosome is here.  A way to view a region which has already been defined is to click on the "Map of Region" button present at the top right of most Individual Record and Summary Table.

• Try viewing a region
• Try viewing a whole chromosome

Chromoscape runs on a user machine in conjunction with the user's browser. After a segment of the genome has been specified, the data is collected from CompDB, a Chromoscape-compatible file is generated, and the file is assembled into the graphic by Chromoscape and displayed in the user's browser. Chromoscape is written in the programming language, Java. Users running Chromoscape 3.0 must run a web browser that supports Java. We recommend the non-beta, Java-capable releases of Netscape and Internet Explorer. Netscape and Internet Explorer can be downloaded using the following links:

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As the graphic is loaded, a new window appears in the browser. It is important not to close the original window or Chromoscape may exit prematurely. A status window also opens and shows how many elements have been loaded. While Chromoscape is a very fast applet, the Internet-based nature of the application means that some maps, especially those that are large or complex, will take some time to load. The speed is dependent upon the power of the user machine, the browser version, and the type of Internet connection.

Once a graphic is loaded and visible on the screen, it can be manipulated in several ways, including:

Selection of elements to retrieve more information
Graphic resizing
Color-coding of elements by type
Changing the order of element type tiers
Graphically highlighting framework to off-framework marker relationships
Searching for elements in a graphic
Printing of a graphic

More detail regarding specific Chromoscape features and how to use them can be found in the following help pages:

• Chromoscape features-Chromoscape application features
• Mouse and keyboard controls-controlling Chromoscape with mouse and keyboard commands
• Menu controls-Features for menu buttons in the Chromoscape application
• Printing from Chromoscape-Printing Chromoscape graphics
• Chromoscape troubleshooting-for solving Chromoscape problems

Chromoscape currently allows the viewing of RH framework markers, RH markers, polymorphic markers, and bundles. Other eGenome features, such as BAC's, PAC's, YAC's, DNA sequence positions, SNP's and cytolocations, can be found as annotations within the individual records for these elements.

All maps are displayed with a framework of well-ordered markers and off-framework markers localized relative to the framework. All displayed elements are selectable (one mouse click) and linked to additional information (two mouse clicks). Select elements to manipulate them in the currently loaded Chromoscape graphic. To obtain additional information about an element, click twice on the element name. This links to the corresponding individual record for that element, which is displayed in a newly opened, separate browser window. For more information about the data displayed in Chromoscape, see the Interpreting maps help section.

Chromoscape is modified from the Genome Database Mapview applet.  Much of the text for the Chromoscape help sections was kindly provided by the Genome Database. The original version of these pages can be found here.

• Chromoscape features
• Menu controls
• Mouse and keyboard controls
• Printing from Chromoscape
• Chromoscape troubleshooting