title: SecretP: identifying bacterial secreted proteins by fusing new features into Chou's pseudo-amino acid composition.
abstract: Protein secretion plays an important role in bacterial lifestyles. Secreted proteins are crucial for bacterial pathogenesis by making bacteria interact with their environments, particularly delivering pathogenic and symbiotic bacteria into their eukaryotic hosts. Therefore, identification of bacterial secreted proteins becomes an important process for the study of various diseases and the corresponding drugs. In this paper, fusing several new features into Chou's pseudo-amino acid composition (PseAAC), two support vector machine (SVM)-based ternary classifiers are developed to predict secreted proteins of Gram-negative and Gram-positive bacteria. For the two types of bacteria, the high accuracy of 94.03% and 94.36% are obtained in distinguishing classically secreted, non-classically secreted and non-secreted proteins by our method. In order to compare the practical ability of our method in identifying bacterial secreted proteins with those of six published methods, proteins in Escherichia coli and Bacillus subtilis are collected to construct the test sets of Gram-negative and Gram-positive bacteria, and the prediction results of our method are comparable to those of existing methods. When performed on two public independent data sets for predicting NCSPs, it also yields satisfactory results for Gram-negative bacterial proteins. The prediction server SecretP can be accessed at http://cic.scu.edu.cn/bioinformatics/secretPV2/index.htm.
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, PR China.
authors.forename: Lezheng
authors.initials: L
authors.lastname: Yu
authors.forename: Yanzhi
authors.initials: Y
authors.lastname: Guo
authors.forename: Yizhou
authors.initials: Y
authors.lastname: Li
authors.forename: Gongbing
authors.initials: G
authors.lastname: Li
authors.forename: Menglong
authors.initials: M
authors.lastname: Li
authors.forename: Jiesi
authors.initials: J
authors.lastname: Luo
authors.forename: Wenjia
authors.initials: W
authors.lastname: Xiong
authors.forename: Wenli
authors.initials: W
authors.lastname: Qin
mesh_terms: D000596:Amino Acids / Q000032:analysis*; D001412:Bacillus subtilis / Q000378:metabolism; D001426:Bacterial Proteins / Q000032:analysis* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000378:metabolism; D006090:Gram-Negative Bacteria / Q000378:metabolism; D006094:Gram-Positive Bacteria / Q000378:metabolism; D020407:Internet; D016571:Neural Networks, Computer
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins