DCGR: feature extractions from protein sequences based on CGR via remodeling multiple information

Abstract

Abstract Background Protein feature extraction plays an important role in the areas of similarity analysis of protein sequences and prediction of protein structures, functions and interactions. The feature extraction based on graphical representation is one of the most effective and efficient ways. However, most existing methods suffer limitations from their method design. Results We introduce DCGR, a novel method for extracting features from protein sequences based on the chaos game representation, which is developed by constructing CGR curves of protein sequences according to physicochemical properties of amino acids, followed by converting the CGR curves into multi-dimensional feature vectors by using the distributions of points in CGR images. Tested on five data sets, DCGR was significantly superior to the state-of-the-art feature extraction methods. Conclusion The DCGR is practically powerful for extracting effective features from protein sequences, and therefore important in similarity analysis of protein sequences, study of protein-protein interactions and prediction of protein functions. It is freely available at https://sourceforge.net/projects/transcriptomeassembly/files/Feature%20Extraction.

Keywords

• Protein feature extraction
• CGR curve
• Physicochemical property
• Algorithm