A major complication for predicting T-cell epitopes through peptide-MHC binding models is MHC polymorphism
. In humans, MHC molecules are known as human leukocyte antigens (HLAs), and there are hundreds of allelic variants of class I (HLA I) and class II (HLA II) molecules.
With the development of study, growing eidence showed that high degrees of MHC polymorphism are closely related to resistance or susceptibility to disease in mammals (Medina et al., 1998; Paterson et al., 1998;Hill et al.,1991;Tang et al., 2012), poultry (Briles et al., 1983; Nikolich-Zugich et al., 2004; Banat et al., 2012) and teleost fish (Zhang et al., 2006b; Wynne et al., 2007; Rakus et al., 2009; Du et al., 2011).
However, only one MHC class II B locus was identified in Chinese long snout catfish (Shen et al., 2011).In mammals, MHC polymorphism is maintained over long times by positive (balancing) selection at the nonsynonymous sites specifying the PBR of the MHC molecule (Graser et al., 1996).