Martina Višňovská, Tomáš Vinař, Broňa Brejová. DNA Sequence Segmentation Based on Local Similarity. In Tomáš Vinař, ed., Information Technologies - Applications and Theory (ITAT), 1003 volume of CEUR-WS, pp. 36-43, 2013.

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DNA sequences evolve by local changes affecting one or several
adjacent symbols, as well as by large-scale rearrangements and
duplications. This results in mosaic sequences with various
degrees of similarity between regions within a single genome or
in genomes of related organisms. Our goal is to segment DNA to
regions and to assign such regions to classes so that regions
within a single class are similar and there is low or no
similarity between regions of different classes. We provide a
formal definition of the segmentation problem, prove its
NP-hardness, and give a practical heuristic algorithm. We have
implemented the algorithm and evaluated it on simulated
data. Segments found by our algorithm can be used as markers in a
wide range of evolutionary studies.