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Protein Subcellular Localization Prediction based on PSI-BLAST Profile and Principal Component Analysis

[ Vol. 16 , Issue. 5 ]

Author(s):

Yuhua Yao*, Manzhi Li , Huimin Xu, Shoujiang Yan, Ping-an He, Qi Dai, Zhaohui Qi and Bo Liao   Pages 400 - 412 ( 13 )

Abstract:


Background: Prediction of protein subcellular location is a meaningful task which attracts much attention in recent years. Particularly, the number of new protein sequences yielded by the highthroughput sequencing technology in the post genomic era has increased explosively.

Objective: Protein subcellular localization prediction based solely on sequence data remains to be a challenging problem of computational biology.

Methods: In this paper, three sets of evolutionary features are derived from the position-specific scoring matrix, which has shown great potential in other bioinformatics problems. A fusion model is built up by the optimal parameters combination. Finally, principal component analysis and support vector machine classifier is applied to predict protein subcellular localization on NNPSL dataset and Cell- PLoc 2.0 dataset.

Results: Our experimental results show that the proposed method remarkably improved the prediction accuracy, and the features derived from PSI-BLAST profile only are appropriate for protein subcellular localization prediction.

Keywords:

Evolutionary information, feature representation, principal component analysis, support vector machine.

Affiliation:

School of Mathematics and Statistics, Hainan Normal University, Haikou 571158, School of Mathematics and Statistics, Hainan Normal University, Haikou 571158, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang 050043, School of Mathematics and Statistics, Hainan Normal University, Haikou 571158



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