Sometimes analyses produce a large amount of data that you might not want to keep displayed in the GI Notebook at all times. Yet, it would be nice to be able to keep the data and refer to it as needed. You can do this by creating an Appendix. Each appendix object resides in its own window which is hidden within the notebook, but can be made visible when you want to see it.

1. Choose Analysis ➧ New Analysis… and choose to do a protein analysis that is called Align 2 Sequences (global) . If you are not sure how to do this, see Tutorial 3: Using Analysis Setups.
2. In the setup panel for this analysis press the button to use scoring table and select the PAM120 table in the Table popup menu. Leave the rest of the settings in this panel at their default values.
3. For input sequences, choose the peptide file Drosophila Hsps and select both Dros hsp26 and Dros hsp27 for the alignment. Please refer to previous tutorials if you are not sure how to do this.
4. Run the analysis by pressing the Run button.
5. The output object that gets placed into your notebook is rather large to begin with and some of the alignment is invisible because it is below the bottom edge of the object. Double-click on the output object to select it. Hold down the option key (Mac) or alt key (Windows) and drag the mouse vertically over the alignment object. The cursor changes to a hand and allows you to move the contents of the object around within the object’s borders. Option/alt-dragging will work in any output object that has more data than is visible within the object boundary.
6. One alternative to option/alt-dragging is to put the object into an appendix windowa. Select the alignment object and then choose Notebook ➧ Appendices ➧ Move Object to Appendices. The dialog shown in Figure 33 will appear. The action you are taking will create a new appendix window to contain the analysis object and also will create a new alias (Mac) or shortcut (Windows) in the GI Notebook to the appendix object. The alias will be placed in the GI Notebook instead of the original object and will “point” to the original object just like an alias in the Finder. Fill in the text in the dialog box to suit your needs and then press OK. You will see an alias that looks like Figure 34.

   Figure 33: Creating an Appendix

   Figure 34: A Notebook Alias Object

7. The resulting GI Notebook alias can be framed or styled just like any other notebook object. To edit the alias text, double-click on the text in the alias and then edit the text.
8. To view the contents of the appendix, either double-click on the appendix icon, or choose the name of the appendix from the Notebook ➧ Appendices submenu. Any appendix you create will be in this menu. By placing information into an appendix, it can be viewed from any place in the notebook. This is a convenient way to store often used information like buffers.
9. To return an appendix to the GI Notebook and remove it from the “appendix” area, choose Notebook ➧ Appendices ➧ Return Appendix to Notebook….
10. You can make an alias to any notebook object (not just an appendix object), including graphics that you import from other programs. This provides a convenient way to refer to the same analysis or object from multiple locations in the notebook. You might also put buffers at specific locations and have aliases to them from anywhere in the notebook. Putting buffers into an appendix is a convenient way to do this.

This concludes this tutorial. You may quit or continue on to the next tutorial. If you choose to continue, close all open windows now.