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

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

According to the method mentioned above, we first associate each of 17 protein sequences in BetaSet with a dimensional vector (cf. Eqs (7) and (8)), and then calculate the pair-wise Euclidean distance between any two of the 17 protein sequences via their m-D vectors. Thus a real symmetric matrix is obtained. On the basis of the achieved distance matrix , a UPGMA tree is constructed using MEGA4 package. The result will depend on values of the rank and the three weight factors. It is found that when , , and , the three non-mammals (Muscovy duck, Gallus and Guttata) form a separate branch and stay outside of the mammals. Moreover, in the subtree of mammals, primate species (Human, Chimpanzee, Gorilla) are grouped closely. Also, rodent species (Norway rat, Spiny mouse, House mouse, Western wild mouse) and lagomorph species (Rabbit, European hare) are situated at independent branches, respectively. While Goat, Sheep, Cattle and Banteng appear to cluster together (Fig. 3) . This result is analogous to that reported in the literature [6, 29, 30, 35, 36] . Accordingly, the four numerical values are respectively used for the four uncertain parameters, and a 31-D feature vector is thus obtained. Fig. (3) . The relationship tree of 17 species.