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Temporal 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:
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Further
Information on TCGRs
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TCGR
Software
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TCGR Images
Publications:
- 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 6th
Symposium on Bioinformatics & Bioengineering (BIBE06), October
16-18, 2006, Washington D.C.
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