On the basis of a selected pair of physicochemical properties of amino acids, we introduce a dynamic 2D graphical representation of protein sequences. Then, we introduce and compare two numerical characterizations of protein graphs as descriptors to analyze the nine ND5 proteins. The approach is simple, convenient, and fast.
Based on the concepts of cell and system of graphical representation, a class of 2D graphical representations of RNA secondary structures are given in terms of classifications of bases of nucleic acids. The representations can completely avoid loss of information associated with crossing and overlapping of the corresponding curve. As an application, we make quantitative comparisons for a set of RNA secondary structures at the 3'-terminus of different viruses based on the graphical representations. The examination of similarities/dissimilarities illustrates the utility of the approach.
Based on the chaos game representation, a 2D graphical representation of protein sequences was introduced in which the 20 amino acids are rearranged in a cyclic order according to their physicochemical properties. The Euclidean distances between the corresponding amino acids from the 2-D graphical representations are computed to find matching (or conserved) fragments of amino acids between the two proteins. Again, the cumulative distance of the 2D-graphical representations is defined to compare the similarity of protein. And, the examination of the similarity among sequences of the ND5 proteins of nine species shows the utility of our approach.
On the basis of a class of 2D graphical representations of DNA sequences, sensitivity analysis has been performed, showing the high-capability of the proposed representations to take into account small modifications of the DNA sequences. And sensitivity analysis also indicates that the absolute differences of the leading eigenvalues of the L/L matrices associated with DNA increase with the increase of the number of the base mutations. Besides, we conclude that the similarity analysis method based on the correlation angles can better eliminate the effects of the lengths of DNA sequences if compared with the method using the Euclidean distances. As application, the examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species has been performed by our method, and the reasonable results verify the validity of our method.
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