The MHC II Epitopes (Sette) track predicts peptide antigenic sites which interact with mouse MHC II haplotype d proteins. There are separate motifs for IAd and IEd haplotypes, and Sette et al., 1989, reports that this method finds more than 75% of known epitope sites for each. However, the method is only effective for x and y motifs for the d haplotype of mouse MHC II proteins. It can be used to design peptide epitopes when used in conjunction with the T-Cell Epitopes – AMPHI and the T-Cell Epitopes – Rothbard-Taylor tracks.
In the Tracks panel, expand Immunogenicity and check the box next to MHC II Epitopes (Sette). 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:
Choose how to set the threshold for a positive IAd region:
- Allow one deleterious substitution – to set it to 400. The is the default choice.
- Allow no deleterious substitutions – to set it to 729.
There are no options available for the IEd method.
Click if you wish to return to the default value.
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