The backbone of the program is the construct, which represents a DNA sequence and all associated sites, regions of interest, segments, comments, and history. The construct can be manipulated and analyzed using four types of windows. Each GCK window visible on the screen corresponds to a file on the disk. The name of the window is the name of the file. There are four kinds of GCK windows: Construct, List, Gel, and Illustration. This are described briefly below and in their own chapters in this manual.

All manipulations of the actual DNA are carried out on the construct within the Construct Window. Restriction enzyme and other sites can be marked, regions of interest can be defined, silent mutations generated, open reading frames found, and the appearance of the construct and its annotations can be edited. The construct can be displayed as linear or circular and either graphically or as a formatted DNA and protein sequence listing.

The List Window is used to create, maintain and edit lists of sequences. The list may contain restriction enzymes, protein binding sites, linkers, promoters, etc. Cut sites can be defined for sequences in the list and comments may be associated with any item in the list. When the list items are used to mark sites in the construct, the comments remain associated with the site.

The Gel Window is used to simulate gel electrophoresis patterns. Any number of digests can be displayed in the Gel Window. Partial digests can be viewed and lanes can be cut and pasted within and between gels. In addition to a graphical view of the gel, the digests can be viewed as tables of fragment size information.

The Illustration Window is used to create documents for presentation or publication, and can also be used to track complex construction projects. Graphics and text from Construct, List, and Gel Windows can be pasted into an Illustration Window and legends can be automatically generated. The Illustration Window also contains a comprehensive set of graphical drawing tools for enhancing illustrations.

Running GCK
GCK is a comprehensive program with many capabilities. The first time you run it, the possibilities might seem so extensive that you are not sure of what to do first. To provide you with an overview of the capabilities and to give you a feel for how the program actually works, you should go through the tutorials. These tutorials are designed to help orient you and will greatly facilitate your understanding of the program and its features while pointing out features you may not think to look for. The time you spend in the tutorials will be repaid many times over in the future as you use GCK.

GCK has a straightforward and intuitive interface with extensive undo capabilities. It has what is called revealed complexity - you can see as much detail as you choose. You should not hesitate to try things for yourself. Select menu options, tool palettes, etc. to see what they do. The Format Menu, in particular, is available from many places within the program and will be useful in ways you might not expect. Besides the tutorials, one of the best ways to learn the capabilities of the Gene Construction Kit is to try new menu options or tools for yourself.

The tutorials introduce you to the Gene Construction Kit. You should do as many of the tutorials as you can because they provide an overview of how the program works. GCK has a number of unique features you might not have seen in any other application -- the tutorials provide a way for you to learn about these unique capabilities. In many locations in this mini-manual you will be asked to select items in menus. To make your choices as clear as possible, all menu selections are indicated as hierarchical choices using a Menu font, such as Edit > Select All. This particular case means to locate the Edit menu and then choose Select All under the Edit menu. Figures in this manual alternate between Windows and Macintosh versions. Note also that the demo version does not allow you to save files or to print. Other than these limitations, the program is completely functional.