Displaying the antigenicity for a protein sequence in a plot is done in the following way:
Toolbox | Protein Analysis ()
| Create Antigenicity Plot ()
This opens a dialog. The first step allows you to add or remove sequences. If you had already selected sequences in the Navigation Area before running the Toolbox action, these are shown in the Selected Elements. Clicking Next takes you through to Step 2, which is displayed in figure 17.3.
The Window size is the width of the window where, the antigenicity is calculated. The wider the window, the less volatile the graph. You can chose from a number of antigenicity scales. Click Next if you wish to adjust how to handle the results. If not, click Finish. The resultcan be seen in figure 17.4.
See Graph preferences for information about the graph view.
The level of antigenicity is calculated on the basis of the different scales. The different scales add different values to each type of amino acid. The antigenicity score is then calculated as the sum of the values in a 'window', which is a particular range of the sequence. The window length can be set from 5 to 25 residues. The wider the window, the less fluctuations in the antigenicity scores.