Geodesic
Investigation of latent periodicity phenomenon in the genomes of eukaryotic organisms
Matematičeskaâ biologiâ i bioinformatika, Tome 13 (2018) no. 3, pp. t84-t103

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Data analysis is presented for the HeteroGenome database first release which contains latent periodicity regions revealed in a number of eukaryotic organisms. Tandem repeats with different integrity of pattern copies, including the highly diverged repeats, have been identified in the genomes of S. cerevisiae, A. thaliana, C. elegans and D. melanogaster. Such data were obtained with the help of original spectral-statistical approach to searching for reliable regions of the latent periodicity in DNA sequences. Special structure of data presentation, consisting of the two levels, was proposed. On the first, nonredundant level the latent periodicity regions are considered as a whole and, additionally, on the second level only conservative elements of their periodic structures are shown. Such data presentation allowed estimating share of the periodicity regions as nearly 10% of the length in analyzed genomes. This estimate was deduced basing on the first level data. Quantitative and qualitative investigation of the latent periodicity regions, their divergence level over all chromosomes of the organisms considered, revealed characteristic types of periodicity in the genome of every organism. Histograms of density distribution for the latent periodicity regions on each chromosome of the genomes analyzed were obtained. Repertoire of period lengths were determinated. The HeteroGenome database has additional possibilities for inner data analysis and is accessible by URL: http://www.jcbi.ru/lp_baze/. 
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     title = {Investigation of latent periodicity phenomenon in the genomes of eukaryotic organisms},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
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}
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M. B. Chaley; V. A. Kutyrkin; E. I. Teplukhina; G. E. Tyulbasheva; N. N. Nazipova. Investigation of latent periodicity phenomenon in the genomes of eukaryotic organisms. Matematičeskaâ biologiâ i bioinformatika, Tome 13 (2018) no. 3, pp. t84-t103. http://geodesic.mathdoc.fr/item/MBB_2018_13_3_a6/

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