Technical Chaos Game Representation (TCGR)

The Temporal Chaos Game Representation (TCGR) of a DNA/RNA sequence is an extension of the FCGR where the frequency of sub-patterns is determined based on a sliding window across the target sequence. A TCGR can be thought of as a two dimensional array with the columns representing the patterns and the rows the window. The rows are ordered in window position order starting at 0. The columns are shown in lexicographic order. This “vertical” view with window position increasing as you move down the image, could be changed to a “horizontal” view with window position moving from left to right. All images we look at in this paper will be vertical. The size of the TCGR depends on the sequence length, the window size, and the size of patterns being examined. There is one row for each window and one column for each sub-pattern being counted. We only count patterns completely contained in each window.

Related information on TCGRs:

· Further Information on TCGRs

· TCGR Software

· TCGR Images

Publications:

1. Margaret H. Dunham, Donya Quick, Yuhang Wang, Monnie McGee, Jim Waddle, “Visualization of DNA/RNA Structure using Temporal CGRs,” to appear in Proceedings of the IEEE 6^th Symposium on Bioinformatics & Bioengineering (BIBE06), October 16-18, 2006, Washington D.C.