Graphical Representation of Proteins

Novel Graphical Representation and Numerical Characterization of DNA Sequences

“…One way to arrive at the numerical characterization of a DNA sequence is to convert its graphical representation into some structural matrices, and use matrix invariants, e.g., the leading eigenvalues, as descriptors of the DNA sequence [8][9][10][11][12][13][14][15][16][17][18]31,32]. It is expected that effective invariants will emerge and enable to uniquely characterize the sequences considered.…”

“…In 2000, Randic et al [8] generalized these 2-D graphical representations to a 3-D graphical representation, in which the center of a cube is chosen as the origin of the Cartesian (x,y,z) coordinate system, and the four corners with coordinates (+1,´1,´1), (´1,+1,´1), (´1,´1,+1), and (+1,+1,+1) are assigned to the four bases. Some other graphical representations of bio-sequences and their applications in the field of biological science and technology can be found in [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24].…”

“…One way to arrive at the numerical characterization of a DNA sequence is to associate the sequence with a vector whose components are related to k-words, including the single nucleotide, dinucleotide, trinucleotide, and so on [25][26][27][28][29][30]. In addition, the numerical characterization can be accomplished by associating with a graphical representation given by a curve in the space (or a plane) structural matrices, such as the Euclidean-distance matrix (ED), the graph theoretical distance matrix (GD), the quotient matrix (D/D, M/M, L/L), and their "higher order" matrices [8][9][10][11][12][13][14][15][16][17][18][31][32][33]. Once a matrix representation of a DNA sequence is given, some matrix invariants, e.g.…”

Rational design of peptide vaccines against the Zika virus through sequence descriptors: Techniques and Problems

“…Numerical characterizations of DNA, RNA and protein sequences provide descriptors that are characteristic of each sequence, albeit depending upon the particular methodology used [5]. Developing upon initial work on DNA sequences, these descriptors have been used to characterize genes to genomes [5] and proteins [6] to proteomes [7], and have seen applications in many areas. While Nandy [8][9][10], Nandy and Nandy [11] and Larionov et al [12] have used 2D graphical systems to determine DNA systematics, Liao et al [13,14] used the novel techniques for alignment-free phylogeny to determine sequence ancestry, Wiesner and Wiesnerova [15] found the new methodology giving better insights into germ-plasm identifiers, Gonzalez-Diaz and his group presented several papers using the concept for alignment-free prediction of polygalacturonases [16], alternative "in silico" technique for chemical research in toxicology [17] and predicting antimicrobial drugs and targets [18], Nandy et al [19] were able to model influenza hemagglutinin and neuraminidase interdependence which provided predictability to new possible viral assortments [20].…”

“…While Nandy [8][9][10], Nandy and Nandy [11] and Larionov et al [12] have used 2D graphical systems to determine DNA systematics, Liao et al [13,14] used the novel techniques for alignment-free phylogeny to determine sequence ancestry, Wiesner and Wiesnerova [15] found the new methodology giving better insights into germ-plasm identifiers, Gonzalez-Diaz and his group presented several papers using the concept for alignment-free prediction of polygalacturonases [16], alternative "in silico" technique for chemical research in toxicology [17] and predicting antimicrobial drugs and targets [18], Nandy et al [19] were able to model influenza hemagglutinin and neuraminidase interdependence which provided predictability to new possible viral assortments [20]. The technique of numerical characterization was extended to proteins initially by Randic et al [21] and led to several approaches being proposed [6,22,23], analyzing phylogenetic relationships between protein families [24], hydropathy profiles of amino acids [25] and others. Thus, numerical characterization of bio-molecular sequences can be considered to have wide-ranging applicability leading to acceptable results, and occasionally new insights.…”