Displaying the hydrophobicity for a protein sequence in a plot is done in the following way:
Toolbox | Protein Analysis ()| Create Hydrophobicity Plot ()
This opens a dialog. The first step allows you to add or remove sequences. If you had already selected a sequence in the Navigation Area, this will be shown in the Selected Elements.Clicking Next takes you through to Step 2, which is displayed in figure 17.5.
The Window size is the width of the window where the hydrophobicity is calculated. The wider the window, the less volatile the graph. You can chose from a number of hydrophobicity scales which are further explained in Bioinformatics explained: Protein hydrophobicity Click Next if you wish to adjust how to handle the results. If not, click Finish. The result can be seen in figure 17.6.
See Graph preferences for information about the graph view.