Bioinformatics Vol. 17 no. 5 2001
Pages 429-437
© 2001 Oxford University Press
Analysis of genomic sequences by Chaos Game Representation
1 ITQB/Universidade Nova Lisboa, PO Box 127,
2780 Oeiras, Portugal
2 Belle W. Baruch Institute for Marine
Biology and Coastal Research, Marine Science Program and Department
of Biological Sciences, University of South Carolina, Columbia, SC
29208, USA
3 Department of Biometry and Epidemiology,
Medical University of South Carolina, PO Box 250551, Charleston, SC
29425, USA
Received on September 20, 2000
; revised on January 5, 2001
; accepted on January 5, 2001
Motivation: Chaos Game Representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to find the coordinates for their position in a continuous space. This distribution of positions has two properties: it is unique, and the source sequence can be recovered from the coordinates such that distance between positions measures similarity between the corresponding sequences. The possibility of using the latter property to identify succession schemes have been entirely overlooked in previous studies which raises the possibility that CGR may be upgraded from a mere representation technique to a sequence modeling tool.
Results: The distribution of positions in the CGR plane were shown to be a generalization of Markov chain probability tables that accommodates non-integer orders. Therefore, Markov models are particular cases of CGR models rather than the reverse, as currently accepted. In addition, the CGR generalization has both practical (computational efficiency) and fundamental (scale independence) advantages. These results are illustrated by using Escherichia coli K-12 as a test data-set, in particular, the genes thrA , thrB and thrC of the threonine operon.
Availability: A web page interface has been created where analyses of arbitrary sequences by CGR can be performed on-line (http://www.itqb.unl.pt:1111/biomat/resources/resources.htm). The test data-set used in this report is also included.
Contact: almeidaj{at}musc.edu; mfletcher{at}biol.sc.edu
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