MHC II Epitopes (Sette)

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.

To apply this track to the sequence:

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

To edit track options:

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.