Abstract
Chaos Game Representation (CGR) of DNA sequences has been used for visual representation as well as alignment-free comparisons. CGR is considered to be of great value as the images obtained from parts of a genome present the same structure as those obtained for the whole genome. However, the robustness of the CGR method to compare DNA sequences obtained in a variety of scenarios is not yet fully demonstrated. This paper addresses this issue by presenting a method to evaluate the potential of CGR to distinguish various classes in a DNA dataset. Two indices are proposed for this purpose - a rejection rate and an overlapping rate. The method was applied to 4 datasets, with between 31 to 400 classes each. Nearly 430 million pairs of DNA sequences were compared using the CGR.
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CITATION STYLE
Marcal, A. R. S. (2018). Evaluation of Chaos Game Representation for Comparison of DNA Sequences. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 11255 LNCS, pp. 179–188). Springer Verlag. https://doi.org/10.1007/978-3-030-05288-1_14
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