a multi-label classifier for predicting the subcellular localization of gram-negative bacterial proteins with both single and multiple sites多标记分类器对革兰氏阴性细菌蛋白质的亚细胞定位预测单个和多个站点.pdfVIP

A Multi-Label Classifier for Predicting the Subcellular Localization of Gram-Negative Bacterial Proteins with Both Single and Multiple Sites 1,2 1 2 Xuan Xiao *, Zhi-Cheng Wu , Kuo-Chen Chou 1 Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen, China, 2 Gordon Life Science Institute, San Diego, California, United States of America Abstract Prediction of protein subcellular localization is a challenging problem, particularly when the system concerned contains both singleplex and multiplex proteins. In this paper, by introducing the ‘‘multi-label scale’’ and hybridizing the information of gene ontology with the sequential evolution information, a novel predictor called iLoc-Gneg is developed for predicting the subcellular localization of Gram-positive bacterial proteins with both single-location and multiple-location sites. For facilitating comparison, the same stringent benchmark dataset used to estimate the accuracy of Gneg-mPLoc was adopted to demonstrate the power of iLoc-Gneg. The dataset contains 1,392 Gram-negative bacterial proteins classified into the following eight locations: (1) cytoplasm, (2) extracellular, (3) fimbrium, (4) flagellum, (5) inner membrane, (6) nucleoid, (7) outer membrane, and (8) periplasm. Of the 1,392 proteins, 1,328 are each with only one subcellular location and the other 64 are each with two subcellular locations, but none of the proteins included has §25% pairwise sequence identity to any other in a same subset (subcellular location). It was observed that the overall success rate by jackknife test on such a stringent benchmark dataset by iLoc-Gneg was over 91%, which is about 6% higher than that by Gneg-mPLoc. As a user- friendly web-server, iLoc-Gneg is freely accessible to the public at /bioinfo/iL