A time-series-based feature extraction approach for prediction of protein structural class

Authors:
Ravi Gupta;Ankush Mittal;Kuldip Singh
Affiliations:
Department of Electronics and Computer Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India and Information Science Division, AU-KBC Research Centre, Anna University, C ...;Department of Electronics and Computer Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India;Department of Electronics and Computer Engineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
Venue:
EURASIP Journal on Bioinformatics and Systems Biology
Year:
2008

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Abstract

This paper presents a novel feature vector based on physicochemical property of amino acids for prediction protein structural classes. The proposed method is divided into three different stages. First, a discrete time series representation to protein sequences using physicochemical scale is provided. Later on, a wavelet-based time-series technique is proposed for extracting features from mapped amino acid sequence and a fixed length feature vector for classification is constructed. The proposed feature space summarizes the variance information of ten different biological properties of amino acids. Finally, an optimized support vector machine model is constructed for prediction of each protein structural class. The proposed approach is evaluated using leave-one-out cross-validation tests on two standard datasets. Comparison of our result with existing approaches shows that overall accuracy achieved by our approach is better than exiting methods.