The T-Cell Epitopes – AMPHI track uses the model of Margalit and Berzofsky, 1987 to predict immunodominant helper T-lymphocyte antigenic sites from primary sequence data. The underlying assumption of the AMPHI method is that T-cell antigenic sites are composed of amphipathic helices. The method is useful only for T-cell epitopes and not B-cell epitopes (the latter normally requires greater knowledge of the tertiary structure of the binding site).
Track results can be displayed as a hydrophobicity graph, an AMPHI region graph, an alpha-helix graph, a 3-10 helix graph (scaled for the amphipathic index) and/or an AMPHI intensity graph. Use the intensity graph to determine the relative intensity of predicted amphipathic regions. For best results, use this method in combination with the MHC II Epitopes and T-Cell Epitopes – Rothbard-Taylor tracks.
In the Tracks panel, expand Immunogenicity, then T-cell epitopes, and then check the box next to AMPHI. The track will now be visible in the Analysis view
Select the track in the Tracks panel. Open the Track Options section, which appears as follows:
- Low amphipathic content – uses a minimum amphipathic index of 4 to create the region graph from three (or more) consecutive regions of length 7. This is the default choice.
- High amphiphatic content – uses an amphipathic index of 8 to create the region plot for three (or more) consecutive regions of length 11. Choose this option only for those proteins known to have high amphipathic content.
Click if you wish to return to the default value.
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