title: Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.
abstract: Bacterial effector proteins secreted by various protein secretion systems play crucial roles in host-pathogen interactions. In this context, computational tools capable of accurately predicting effector proteins of the various types of bacterial secretion systems are highly desirable. Existing computational approaches use different machine learning (ML) techniques and heterogeneous features derived from protein sequences and/or structural information. These predictors differ not only in terms of the used ML methods but also with respect to the used curated data sets, the features selection and their prediction performance. Here, we provide a comprehensive survey and benchmarking of currently available tools for the prediction of effector proteins of bacterial types III, IV and VI secretion systems (T3SS, T4SS and T6SS, respectively). We review core algorithms, feature selection techniques, tool availability and applicability and evaluate the prediction performance based on carefully curated independent test data sets. In an effort to improve predictive performance, we constructed three ensemble models based on ML algorithms by integrating the output of all individual predictors reviewed. Our benchmarks demonstrate that these ensemble models outperform all the reviewed tools for the prediction of effector proteins of T3SS and T4SS. The webserver of the proposed ensemble methods for T3SS and T4SS effector protein prediction is freely available at http://tbooster.erc.monash.edu/index.jsp. We anticipate that this survey will serve as a useful guide for interested users and that the new ensemble predictors will stimulate research into host-pathogen relationships and inspiration for the development of new bioinformatics tools for predicting effector proteins of T3SS, T4SS and T6SS.
authors: Yi
authors: Y
authors: An
authors: Jiawei
authors: J
authors: Wang
authors: Chen
authors: C
authors: Li
authors: André
authors: A
authors: Leier
authors: Tatiana
authors: T
authors: Marquez-Lago
authors: Jonathan
authors: J
authors: Wilksch
authors: Yang
authors: Y
authors: Zhang
authors: Geoffrey I
authors: GI
authors: Webb
authors: Jiangning
authors: J
authors: Song
authors: Trevor
authors: T
authors: Lithgow
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism; D001419:Bacteria / Q000254:growth & development / Q000378:metabolism*; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D058947:Bacterial Secretion Systems / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D054884:Host-Pathogen Interactions; D006801:Humans; D056510:Position-Specific Scoring Matrices; D012984:Software
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D058947:Bacterial Secretion Systems
keywords: bacterial secretion system; effector protein; logistic regression; random forest; support vector machine