Chen Dong, Li Yanjuan
College of Electrical and Information Engineering, Quzhou University, Quzhou, China.
Front Genet. 2022 Apr 25;13:875112. doi: 10.3389/fgene.2022.875112. eCollection 2022.
The major histocompatibility complex (MHC) is a large locus on vertebrate DNA that contains a tightly linked set of polymorphic genes encoding cell surface proteins essential for the adaptive immune system. The groups of proteins encoded in the MHC play an important role in the adaptive immune system. Therefore, the accurate identification of the MHC is necessary to understand its role in the adaptive immune system. An effective predictor called PredMHC is established in this study to identify the MHC from protein sequences. Firstly, PredMHC encoded a protein sequence with mixed features including 188D, APAAC, KSCTriad, CKSAAGP, and PAAC. Secondly, three classifiers including SGD, SMO, and random forest were trained on the mixed features of the protein sequence. Finally, the prediction result was obtained by the voting of the three classifiers. The experimental results of the 10-fold cross-validation test in the training dataset showed that PredMHC can obtain 91.69% accuracy. Experimental results on comparison with other features, classifiers, and existing methods showed the effectiveness of PredMHC in predicting the MHC.
主要组织相容性复合体（MHC）是脊椎动物DNA上的一个大位点，它包含一组紧密连锁的多态基因，这些基因编码适应性免疫系统所必需的细胞表面蛋白。MHC中编码的蛋白质组在适应性免疫系统中发挥着重要作用。因此，准确识别MHC对于理解其在适应性免疫系统中的作用至关重要。本研究建立了一种名为PredMHC的有效预测器，用于从蛋白质序列中识别MHC。首先，PredMHC对具有混合特征的蛋白质序列进行编码，这些特征包括188D、APAAC、KSCTriad、CKSAAGP和PAAC。其次，使用蛋白质序列的混合特征对包括SGD、SMO和随机森林在内的三种分类器进行训练。最后，通过三种分类器的投票获得预测结果。训练数据集中10倍交叉验证测试的实验结果表明，PredMHC可以获得91.69%的准确率。与其他特征、分类器和现有方法比较的实验结果表明，PredMHC在预测MHC方面是有效的。
