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.
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.
Need more help with this?