CLC Genomics Workbench can help to identify antigenic regions in protein sequences in different ways, using different algorithms. The algorithms provided in the Workbench, merely plot an index of antigenicity over the sequence.

Two different methods are available:

Note! Similar results from the two methods can not always be expected as the two methods are based on different training sets.

Displaying the antigenicity for a protein sequence in a plot is done in the following way:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Protein Analysis (Image proteinanalyses) | Create Antigenicity Plot (Image graph)

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 20.3.

Image antigenicityPlotStep2
Figure 20.3: Step two in the Antigenicity Plot allows you to choose different antigenicity scales and the window size.

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 Finish to start the tool. The resultcan be seen in figure 20.4.

Image antigenicityplotfinal
Figure 20.4: The result of the antigenicity plot calculation and the associated Side Panel.

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.

Antigenicity graphs along the sequence can be displayed using the Side Panel. The functionality is similar to hydrophobicity along the sequence.