Predicting Protein Subcellular Localization by Pseudo Amino Acid Composition with a Segment-Weighted and Features-Combined Approach

被引:15
|
作者
Wang, Wei [1 ]
Geng, XingBo [2 ]
Dou, Yongchao [2 ]
Liu, Taigang [3 ]
Zheng, Xiaoqi [1 ,4 ]
机构
[1] Shanghai Normal Univ, Dept Math, Shanghai 200234, Peoples R China
[2] Dalian Univ Technol, Dept Appl Math, Dalian 116024, Peoples R China
[3] Shandong Agr Univ, Coll Informat Sci & Engn, Tai An 271018, Shandong, Peoples R China
[4] Sci Comp Key Lab Shanghai Univ, Shanghai 200234, Peoples R China
来源
PROTEIN AND PEPTIDE LETTERS | 2011年 / 18卷 / 05期
基金
中国国家自然科学基金;
关键词
Jackknife test; mature protein; optimal splice site; pseudo amino acid composition; sorting signal; subcellular localization; SUPPORT VECTOR MACHINES; FUNCTIONAL DOMAIN COMPOSITION; STRUCTURAL CLASS PREDICTION; ENZYME SUBFAMILY CLASSES; LOCATION PREDICTION; SIGNAL PEPTIDES; APOPTOSIS PROTEINS; CLEAVAGE SITES; TRANSMEMBRANE PROTEINS; APPROXIMATE ENTROPY;
D O I
10.2174/092986611794927947
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Information of protein subcellular location plays an important role in molecular cell biology. Prediction of the subcellular location of proteins will help to understand their functions and interactions. In this paper, a different mode of pseudo amino acid composition was proposed to represent protein samples for predicting their subcellular localization via the following procedures: based on the optimal splice site of each protein sequence, we divided a sequence into sorting signal part and mature protein part, and extracted sequence features from each part separately. Then, the combined features were fed into the SVM classifier to perform the prediction. By the jackknife test on a benchmark dataset in which none of proteins included has more than 90% pairwise sequence identity to any other, the overall accuracies achieved by the method are 94.5% and 90.3% for prokaryotic and eukaryotic proteins, respectively. The results indicate that the prediction quality by our method is quite satisfactory. It is anticipated that the current method may serve as an alternative approach to the existing prediction methods.
引用
收藏
页码:480 / 487
页数:8
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