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

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

Using the above-determined values for parameters , w 1 , w 2 , and w 3 , we calculate the 31-D feature vectors of 72 coronavirus spike proteins and their Euclidean distance matrix; then the corresponding phylogenetic tree (Fig. 4) is constructed. Observing Fig. (4) , we find that the 72 coronavirus spike proteins are clustered into three groups: one contains the five alpha coronaviruses (PEDVC, PEDV, TGEVG, TGEV, and HCoV-229E), the second includes the three gamma coronaviruses (IBV, IBVBJ, IBVC), and the third corresponds to the group beta. A closer look at the subtree of beta coronaviruses shows that MERS-CoVs are clearly clustered together, so it is with SARS-CoVs, while MHV, MHVA, MHVM, MHVP, MHVJHM, BCoV, BCoVE, BCoVL, BCoVM, BCoVQ and HCoV-OC43 are situated at an independent branch. The resulting cluster agrees well with the established taxonomic groups.