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Predicting protein-protein interactions between banana and Fusarium oxysporum f. sp. cubense race 4 integrating sequence and domain homologous alignment and neural network verification

文献类型： 外文期刊

作者： Fang, Hui 1 ; Zhong, Cheng 1 ; Tang, Chunyan 2 ;

作者机构： 1.Guangxi Univ, Med Coll, State Key Lab Conservat & Utilizat Subtrop Agrobi, Nanning 530004, Guangxi, Peoples R China

2.Guangxi Univ, Sch Comp Elect & Informat, Nanning 530004, Guangxi, Peoples R China

3.Guangxi Acad Agr Sci, Guangxi Crop Genet Improvement & Biotechnol Lab, Nanning 530007, Guangxi, Peoples R China

关键词： Protein-protein interactions; Banana; Fusarium oxysporum f; sp; cubense race 4; Sequence alignment; Prediction

期刊名称：PROTEOME SCIENCE （ 影响因子：2.882； 五年影响因子：3.041 ）

ISSN：

年卷期： 2022 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background The pathogen of banana Fusarium oxysporum f. sp. cubense race 4(Foc4) infects almost all banana species, and it is the most destructive. The molecular mechanism of the interactions between Fusarium oxysporum and banana still needs to be further investigated. Methods We use both the interolog and domain-domain method to predict the protein-protein interactions (PPIs) between banana and Foc4. The predicted protein interaction sequences are encoded by the conjoint triad and autocovariance method respectively to obtain continuous and discontinuous information of protein sequences. This information is used as the input data of the neural network model. The Long Short-Term Memory (LSTM) neural network five-fold cross-validation and independent test methods are used to verify the predicted protein interaction sequences. To further confirm the PPIs between banana and Foc4, the GO (Gene Ontology) and KEGG (Kyoto Encylopedia of Genes and Genomics) functional annotation and interaction network analysis are carried out. Results The experimental results show that the PPIs for banana and foc4 predicted by our proposed method may interact with each other in terms of sequence structure, GO and KEGG functional annotation, and Foc4 protein plays a more active role in the process of Foc4 infecting banana. Conclusions This study obtained the PPIs between banana and Foc4 by using computing means for the first time, which will provide data support for molecular biology experiments.

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