C-curve: A novel 3D graphical representation of DNA sequence based on codons

A 2D Graphical Representation of the Sequences of DNA Based on Triplets and Its Application

“…It is consistent with the fact that Gallus is not a mammal, whereas the others [2,5,7,9,33]. For testing the validity of our method, the existing results of the examination of the degree of similarity/ dissimilarity of the coding sequences of β-globin genes of several species with the coding sequence of the human β-globin gene by means of approaches using alternative DNA sequence descriptors [2,5,7,9] are listed in Table 6 for comparison.…”

“…From Table 6, we can find that the pairs like humangorilla and human-chimpanzee are the two most similar species pairs when adopting (A) the method of our work, (B) the method of [2], (C) the method of [5], and (D) the method of [7], which is in accordance with the fact that gorilla and chimpanzee are the two most closest species of human, but when adopting (E) the method of [9], the most similar species pair is human-goat, which is obviously not correct. In addition, the pairs like human-Gallus and human-opossum are the two most dissimilar species pairs when adopting (A) the method of our work, (C) the method of [5], and (E) the method of [9], which is in accordance with the fact that Gallus is not a mammal, whereas the others are mammals, and opossum is the most remote species from the remaining mammals.…”

“…For any two given complete coding sequences A and B, suppose that their triplet-repeat model sets are {<T 1 , X 1 >, <T 2 , X 2 >,…, <T 64 , X 64 >} and {<T 1 , Y 1 >, <T 2 , Y 2 >,…, <T 64 , Y 64 >}, respectively. Then, on the basis of the 2D graphical representation given in the previous Section 2, we can define the weight deviation between the two DNA sequences A and B as the following formula (2) to measure the similarity between A and B.…”

“…Recently, graphical representation is well regarded which can offer visual inspection of data and provide a simple way to facilitate the similarity analysis and comparison of DNA sequences [1][2][3][4][5]. Because of its convenience and excellent maneuverability, currently, all kinds of methods based on graphical representation have been extensively applied in relevant realms of bioinformatics.…”

Graphical Representation of Biological Sequences

“…The assignments of this type (including the variations with some modifications) are utilized in Refs. [26,27,29,[31][32][33][34][35][36].…”