For each of 381 protein sequences, the sequences of proteins were input to NetMHCIIpan 3.2 server (Jensen et al. 2018) to predict the peptides, which could bind to MHC-II molecule. The length of screened peptides was set as 15-mer. The peptides with predicted binding affinity with MHC-II molecule raTnked in top 2% were defined as strong binding peptides. The weak binding peptides referred to the peptides with top 10% ranked binding affinity. All of the available peptides in each protein were screened and the binding ability between peptides and the MHC-II subtypes including H-2-IAb, H-2-IEb, H-2-IAd, and H-2-IEd were predicted. In this model, the significant peptides SII was defined, if the peptides could bind to more than half of selected MHC-II subtypes.

For protein P, MHC-II binding peptide sore MIIP was defined as formula (2).

where SII represents significant MHC-II binding peptides included in protein P.N(SII) refers to the number of SII. And len(P) represents the length of protein P.

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