This chapter contains a number of tutorials introducing you to Gene Inspector®. Although you should not feel obligated to going through all the tutorials, you should do as many of the tutorials as you can because they are designed to provide an overview of how the program works. Doing the tutorials now will save you many hours in the future. The Gene Inspector 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 chapter and throughout the 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 ➧. This particular case means to locate the menu and then choose under the menu.
About the Tutorials
There are three major parts of Gene Inspector: the GI Notebook, the sequence editor, and the analysis setups. These three parts are dealt with individually in the first three tutorials. If you do not have time to do any other tutorials, you should at least complete the first three which illustrate these components of Gene Inspector. See Tutorial 4: Hotlinking Analysis Results is also important in demonstrating how the analysis results in your notebook are alive and connected to the original sequences used for the analysis. Other tutorials help explain different capabilities of Gene Inspector and demonstrate ways in which the program might be of special use to you.
Selection vs. Target
The difference between choosing an object as a selection or a target within the Gene Inspector is important . The terms are specific and each will allow you to perform a different set of specific functions on an object. These terms are used throughout the manual and are important for you to know. The two choices are shown in Figure 1.
Figure 1: Selection vs. Target
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Clicking once on a GI Notebook object makes it the selection and causes the appearance of eight "handles" (little black squares at the corners and midway along each side) around the edges of the object (left part of figure). You can resize the object using these handles in the same way you would within a standard drawing program.
Double-clicking on a GI Notebook analysis object makes it the target and causes the appearance of a gray border around the object (right part of figure). Once an object is targeted, you can modify components within the object and can use the features available in the menu which appears when an object is targeted.
Sequences
You will be using a number of DNA and protein sequences in these tutorials. They are all saved in a folder called "GI Seqs" which was placed in the "Gene Inspector folder" folder during installation. Within the GI Seqs folder, there is a peptide folder and a DNA folder. Each file may contain multiple sequences (for example, see Figure 6).
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