Chaos creates a chaos game representation (CGR) plot for a nucleotide sequence. A CGR plot represents a nucleotide sequence as a square box with an A, G, C, or T nucleotide at each corner.
The box contains dots, each one representing a dinucleotide. All overlapping dinucleotides from the start to the end of the sequence are plotted.
Regions which are devoid of dots (or heavily covered with dots) indicate short sequence motifs that are unusually infrequent (or frequent).
CGR plots depict base composition and sequentiality and is a unique visual representation of a sequence that complements more traditional linear representations.
Algorithm
The plot is generated as follows. A box is drawn and an A, G, C, or T is drawn at each corner. Starting from the middle, move half way to the corner of the box representing the first base in the sequence and draw a dot. Then for each subsequent base move half way to the corresponding box corner and draw a dot. Finally display the number and percentage values of AGCT bases. The result is an image of a square sprinkled with dots.
D29
L5
Bxz2
TM4 
