PREDICTING SUBCHLOROPLAST LOCATIONS OF PROTEINS BASED ON THE GENERAL FORM OF CHOU＇S PSEUDO AMINO ACID COMPOSITION： APPROACHED FROM OPTIMAL TRIPEPTIDE COMPOSITION
PREDICTING SUBCHLOROPLAST LOCATIONS OF PROTEINS BASED ON THE GENERAL FORM OF CHOU＇S PSEUDO AMINO ACID COMPOSITION： APPROACHED FROM OPTIMAL TRIPEPTIDE COMPOSITION作者机构：Key Laboratory for Neurolnformation of Ministry of EducationCenter of Bioinformatics School of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 P. R. China
出 版 物：《International Journal of Biomathematics》 (生物数学学报（英文版）)
年 卷 期：2013年第6卷第2期
页 面：47-60页
学科分类：0710[理学-生物学] 0821[工学-纺织科学与工程] 071010[理学-生物化学与分子生物学] 081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 082101[工学-纺织工程]
主 题：Subchloroplast localization tripeptide binomial distribution support vectormachine.
摘 要：Chloroplasts are organelles found in plant cells that conduct photosynthesis. The subchloroplast locations of proteins are correlated with their functions. With the availability of a great number of protein data, it is highly desired to develop a com- putational method to predict the subchloroplast locations of chloroplast proteins. In this study, we proposed a novel method to predict subchloroplast locations of proteins using tripeptide compositions. It first used the binomial distribution to optimize the feature sets. Then the support vector machine was selected to perform the prediction of subchloroplast locations of proteins. The proposed method was tested on a reliable and rigorous dataset including 259 chloroplast proteins with sequence identity ≤ 25%. In the jack-knife cross-validation, 92.21% envelope proteins, 93.20% thylakoid mem- brane, 52.63% thylakoid lumen and 85.00% stroma can be correctly identified. The overall accuracy achieves 88.03% which is higher than that of other models. Based on this method, a predictor called ChloPred has been built and can be freely available from http：//***/people/hlin/tools/ChloPred/. The predictor will provide important information for theoretical and experimental research of chloroplast proteins.
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