DV-Curve Representation of Protein Sequences and Its Application

DV-Curve Representation of Protein Sequences and Its Application

Wei Deng, Yihui Luan

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.

2014

DOI: 10.1155/2014/203871

Computational and Mathematical Methods in Medicine

Hindawi Limited

Computer applications to medicine. Medical informatics