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

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.