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Geary autocorrelation and DCCA coefficient: Application to predict apoptosis protein subcellular localization via PSSM

Yunyun Liang, Sanyang Liu and Shengli Zhang

Physica A: Statistical Mechanics and its Applications, 2017, vol. 467, issue C, 296-306

Abstract: Apoptosis is a fundamental process controlling normal tissue homeostasis by regulating a balance between cell proliferation and death. Predicting subcellular location of apoptosis proteins is very helpful for understanding its mechanism of programmed cell death. Prediction of apoptosis protein subcellular location is still a challenging and complicated task, and existing methods mainly based on protein primary sequences. In this paper, we propose a new position-specific scoring matrix (PSSM)-based model by using Geary autocorrelation function and detrended cross-correlation coefficient (DCCA coefficient). Then a 270-dimensional (270D) feature vector is constructed on three widely used datasets: ZD98, ZW225 and CL317, and support vector machine is adopted as classifier. The overall prediction accuracies are significantly improved by rigorous jackknife test. The results show that our model offers a reliable and effective PSSM-based tool for prediction of apoptosis protein subcellular localization.

Keywords: Subcellular location; Geary autocorrelation; DCCA coefficient; Position-specific scoring matrix; Support vector machine (search for similar items in EconPapers)
Date: 2017
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Handle: RePEc:eee:phsmap:v:467:y:2017:i:c:p:296-306