Journal
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
Volume 1813, Issue 3, Pages 424-430Publisher
ELSEVIER
DOI: 10.1016/j.bbamcr.2011.01.011
Keywords
Submitochondria locations; Subchloroplast locations; Discrete wavelet transform; Support vector machine; Pseudo amino acid composition
Categories
Funding
- National Natural Science Foundation of China [20605010, 20865003, 20805023]
- Jiangxi Province Natural Science Foundation [2007JZH2644]
- Opening Foundation of State Key Laboratory of Chem/Biosensing and Chemometrics of Hunan University [2006022]
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It is very challenging and complicated to predict protein locations at the sub-subcellular level. The key to enhancing the prediction quality for protein sub-subcellular locations is to grasp the core features of a protein that can discriminate among proteins with different subcompartment locations. In this study, a different formulation of pseudoamino acid composition by the approach of discrete wavelet transform feature extraction was developed to predict submitochondria and subchloroplast locations. As a result of jackknife cross-validation, with our method, it can efficiently distinguish mitochondrial proteins from chloroplast proteins with total accuracy of 98.8% and obtained a promising total accuracy of 93.38% for predicting submitochondria locations. Especially the predictive accuracy for mitochondrial outer membrane and chloroplast thylakoid lumen were 82.93% and 82.22%, respectively, showing an improvement of 4.88% and 27.22% when other existing methods were compared. The results indicated that the proposed method might be employed as a useful assistant technique for identifying sub-subcellular locations. We have implemented our algorithm as an online service called SubIdent (http://bioinfo.ncu.edu.cn/services.aspx). (c) 2011 Elsevier B.V. All rights reserved.
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