Protein Sequence Comparison and DNA-binding Protein Identification with Generalized PseAAC and Graphical Representation

Li, Chun; Zhao, Jialing; Wang, Changzhong; Yao, Yuhua

Based on two important physicochemical properties, 20 standard amino acids were distributed into three groups, and to each of which a representative symbol was assigned. By replacing each amino acid with its representative letter, a protein primary sequence was converted into a three-letter sequence, which can be viewed as a coarse-grained description of the protein primary sequence. On the basis of the three-letter sequence, a graph without loops and multiple edges was obtained. By taking the advantage of the 2-D graph, we constructed a geometric line adjacency matrix (GLAM) and then the corresponding ALE-index, the lineadjacency index, the first Zagreb index and its modification were calculated. In addition, order-correlated factors were extracted via the reduced sequence. By combining these elements with the frequencies of occurrence of 20 standard amino acids and their three representative letters, a generalized PseAAC model of a protein sequence was constructed. On five popular datasets, the proposed method was tested by phylogenetic analysis and identification of DNA-binding proteins. The results illustrated the better performance of our method.