title: DV-curve representation of protein sequences and its application.
abstract: Based on the detailed hydrophobic-hydrophilic(HP) model of amino acids, we propose dual-vector curve (DV-curve) representation of protein sequences, which uses two vectors to represent one alphabet of protein sequences. This graphical representation not only avoids degeneracy, but also has good visualization no matter how long these sequences are, and can reflect the length of protein sequence. Then we transform the 2D-graphical representation into a numerical characterization that can facilitate quantitative comparison of protein sequences. The utility of this approach is illustrated by two examples: one is similarity/dissimilarity comparison among different ND6 protein sequences based on their DV-curve figures the other is the phylogenetic analysis among coronaviruses based on their spike proteins.
authors.affiliation: School of Mathematics, Shandong University, Jinan 250100, China ; School of Science, Shandong Jianzhu University, Jinan 250101, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.affiliation: School of Mathematics, Shandong University, Jinan 250100, China.
authors.forename: Yihui
authors.initials: Y
authors.lastname: Luan
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003198:Computer Simulation; D017934:Coronavirus / Q000378:metabolism; D004247:DNA / Q000737:chemistry; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D051379:Mice; D008962:Models, Theoretical; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry*; D051381:Rats; D015203:Reproducibility of Results
chemical_list: D000596:Amino Acids; D011506:Proteins; D004247:DNA