Three Dimensional Chaos Game Representation of Genomic Sequences

Chaos game representation (CGR) has been proposed as a method to convert genomic sequences to scale-independent and unique images. Many useful properties and applications have been indicated for these images. In this paper, a new procedure for three- dimensional visualization of genomic sequences is introduced based on Chaos Game Representation algorithm. In this method instead of four points as four bases in nucleotide sequences, eight points are considered as eight corners of a cube. Four different nucleotides in protein coding regions of the sequence (A, C, G and T) and four different nucleotides in non- coding regions (A, C, G and T) are eight corners of the cube. The mapping equations of chaos game for eight points in three dimensional space (a cube) is used to convert a genomic sequence to a three dimensional image. This visualization can be used for analysis of whole genomes based on coding and no-coding regions.