Minimal-dot plot: "Old tale in new skin" about sequence comparison

Authors:
V. Kirzhner;S. Frenkel;A. Korol
Affiliations:
Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 31905, Israel;Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 31905, Israel;Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 31905, Israel
Venue:
Information Sciences: an International Journal
Year:
2011

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Abstract

The authors propose a simple version of the dot-plot scheme to be used in the case when the distances between sequence elements may take more than two values. The method is applicable, in particular, to the case of the sequences of large-length windows when the sets of distance values are continuous. The proposed technique is simple to implement and the results can produce readable maps for further analysis. To illustrate its potentialities, the method has been applied to the comparison of genomic sequences. The asymmetry in the number of direct and reverse tracks for the Homo sapience genome has been discovered.