一种快速准确区分Ⅲ型、Ⅳ型分泌效应蛋白的计算方法

A fast and accurate computational approach for the distinction of typeⅢandⅣsecreted effector proteins

通过Ⅲ型、Ⅳ型、Ⅵ型分泌系统,革兰氏阴性菌可将效应蛋白直接注入宿主体内,并导致宿主感染各种疾病.由于Ⅲ型、Ⅳ型分泌效应蛋白均属非经典分泌蛋白,且它们可能具有相似的序列模体或进化保守性,故两者之间难于区分.基于支持向量机和伪位置特异性得分矩阵,本文提出了一种可快速准确识别革兰氏阴性菌Ⅲ型、Ⅳ型效应蛋白的计算方法.测试集实验结果表明,本方法对Ⅲ型、Ⅳ型效应蛋白具有较好的分类效果,可作为辅助工具用于分泌效应蛋白的进一步研究.

Through typeⅢ,Ⅳ,Ⅵsecretion systems,Gram-negative bacterial effector proteins can be directly injected into host cells,which causes the hosts infected with various diseases.Because both of typeⅢ,Ⅳsecreted effector proteins belong to the non-classically secreted proteins(NCSPs),and may have similar sequence motifs or evolutionary conservation profiles,it is hard to distinguish them from each other.Based on support vector machine(SVM)and pseudo position specific scoring matrix(PsePSSM),a computational approach is proposed to fastly and accurately classify the typeⅢandⅣeffector proteins of Gram-negative bacteria.The test results show that this approach has a good effect on the classification of typeⅢandⅣeffector proteins,and could be used as a supplementary tool for further studies of secreted effector proteins.