A new 3D graphical representation for similarity/dissimilarity studies of protein sequences

Yan Chen, Kang-Shun Li, Shan Chang, Lei Yang

COMPUTER MODELLING & NEW TECHNOLOGIES 2014 18(12D) 296-303

College of Information, South China Agricultural University, Guangzhou 510642, China

With the development of sequencing technology and the rapid growing number of protein sequences, how to find useful information from these large numbers of protein sequences has become an important research focus. The dominant factor of protein’s characteristic is each amino acid of it. So this paper uses three-dimensional Cartesian coordinate system to represent three important physical chemistry properties of amino acids: hydrophobicity of amino acids, aromatic amino acids, and side-chain conformations.A new 3D graphical representation of protein sequences is proposed, based on the analysis. Using this graphical approach, 1D sequence of the protein can be expressed as a 3D graphics. At the same time, the similarity comparison of protein-sequences, prediction of functional sites, and other sequence analysis operations can be done further. The paper selects 15 protein sequences of ND6 to conduct the experiment, and the result shows that the analysis of the structures is consistent with the actual results of biological evolution. The experiment illustrates the utility of our approach.