Similarity/dissimilarity analysis of protein sequences using the spatial median as a descriptor

Mervat M. Abo-Elkhier

Department of Engineering Mathematics and Physics, Faculty of Engineering, Mansoura University, Mansoura, Egypt.

DOI: 10.4236/jbpc.2012.32016                

Abstract

A novel 3-D graphical representation of protein sequence has been introduced. A right cone of a unit base and unit height has been selected to represent protein sequences on its surface. The twenty amino acids have been represented by 20 circles and all protein's residues have been represented by n lines on the cone's surface. All the spots which represent the protein's residues have been shown in the cone's top view. The spatial median of all the spots is used as a new descriptor of any protein sequence. This approach was applied on two short segments of protein of yeast Saccharomyces cerevisiae. The examination of the similarities/dissimilarities for the eight ND5 proteins and the six β-globin proteins illustrate the utility of our approach. A linear correlation and significance analysis have been provided to compare our results and the percentage sequence alignment identity.

Keywords

Right Cone; Non Equal Proteins; Spatial Median; Similarity/Dissimilarity; Linear Correlation and Significance Analysis

Conflicts of Interest

The authors declare no conflicts of interest.

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