☆ 4.3 Article

PREDICTING SUBCHLOROPLAST LOCATIONS OF PROTEINS BASED ON THE GENERAL FORM OF CHOU'S PSEUDO AMINO ACID COMPOSITION: APPROACHED FROM OPTIMAL TRIPEPTIDE COMPOSITION

INTERNATIONAL JOURNAL OF BIOMATHEMATICS (2013)

Journal

INTERNATIONAL JOURNAL OF BIOMATHEMATICS

Volume 6, Issue 2, Pages -

Publisher

WORLD SCIENTIFIC PUBL CO PTE LTD

DOI: 10.1142/S1793524513500034

Keywords

Subchloroplast localization; tripeptide; binomial distribution; support vector machine

Categories

Mathematical & Computational Biology

Funding

Fundamental Research Funds for the Central Universities [ZYGX2012J113]
Project of Education Department in Sichuan [12ZA112]
National Natural Science Foundation of China [61202256, 61100092]

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Abstract

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 computational 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 membrane, 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://cobi.uestc.edu.cn/people/hlin/tools/ChloPred/. The predictor will provide important information for theoretical and experimental research of chloroplast proteins.

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