Displaying the hydrophobicity for a protein sequence in a plot is done in the following way:
Toolbox | Classical Sequence Analysis () | 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 16.11.
Figure 16.11: Step two in the Hydrophobicity Plot allows you to choose hydrophobicity scale and the window size.
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 16.12.
Figure 16.12: The result of the hydrophobicity plot calculation and the associated Side Panel.
See Graph preferences for information about the graph view.