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[Text] / M. Sadovsky, A. Chernyshova ; ed. S. . Battiston [et al.] // PROCEEDINGS OF ECCS 2014: EUROPEAN CONFERENCE ON COMPLEX SYSTEMS : SPRINGER, 2016. - European Conference on Complex Systems (ECCS) (SEP 22-26, 2014, IMT Sch Adv Studies Lucca, Lucca, ITALY). - P59-68. - (Springer Proceedings in Complexity), DOI 10.1007/978-3-319-29228-1_6. - Cited References:21 . - ISBN 978-3-319-29228-1; 978-3-319-29226-7РУБ Computer Science, Theory & Methods + Mathematics, Applied

Аннотация: The distribution of chloroplast genomes in 63-dimensional space of triplet frequencies was studied, in connection to the taxonomy correlation to the clusters observed in the distribution. That latter was developed through K-means implementation, for the number of classes varying from 2 to 8. The clade composition of those clusters has been analyzed. Unexpectedly high regularity in clades occupation of different clusters has been found thus proving very high synchrony in evolution of two physically independent genetic entities (chloroplasts vs. nuclear genomes): the proximity in frequency space was determined over the organelle genomes, while the proximity in taxonomy was determined morphologically.

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Держатели документа:
Inst Computat Modelling SB RAS, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.

Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Chernyshova, Anna

/ M. G. Sadovsky, M. Y. Senashova, A. V. Malyshev // Zhurnal Obshchei Biol. - 2018. - Vol. 79, Is. 2. - С. 124-134. - Cited References:14 . - ISSN 0044-4596РУБ Biology

Аннотация: It is tested whether seven-cluster genome structure, detected in bacteria, is a universal one and whether all of its observed properties pertain to other genomes. Inner structuring of chloroplasts' and cyanobacteria's genome is studied, and it is found out that this structuring notably differs from what was earlier discovered in bacterial genomes. By structuring it is meant the clasterization of triplet frequency dictionary developed for different genome fragments which have regular allocation, independent of the fragment function. The clasterization has been executed by the method of elastic maps.

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Держатели документа:
RAS, Inst Computat Modelling, Siberian Branch, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Sch Fundamental Biol & Biotechnol, Svobodny Pr 79, Krasnoyarsk 660041, Russia.

Доп.точки доступа:
Sadovsky, M. G.; Senashova, M. Yu.; Malyshev, A. V.

/ M. G. Sadovsky, M. Y. Senashova, A. V. Malyshev // BMC Bioinformatics. - 2020. - Vol. 21. - Ст. 83, DOI 10.1186/s12859-020-3350-z. - Cited References:45 . - ISSN 1471-2105РУБ Biochemical Research Methods + Biotechnology & Applied Microbiology

Аннотация: Background Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast genomes. Results Surprisingly, eight cluster structure has been found, for chloroplasts. The pattern observed for chloroplasts differs rather significantly, from bacterial one, and from that latter observed for cyanobacteria. The structure is provided by clustering of the fragments of equal length isolated within a genome so that each fragment is converted in triplet frequency dictionary with non-overlapping triplets with no gaps in frame tiling. The points in 63-dimensional space were clustered due to elastic map technique. The eight cluster found in chloroplasts comprises the fragments of a genome bearing tRNA genes and exhibiting excessively high GC-content, in comparison to the entire genome. Conclusion Chloroplasts exhibit very specific symmetry type in distribution of coding and non-coding fragments of a genome in the space of triplet frequencies: this is mirror symmetry. Cyanobacteria may have both mirror symmetry, and the rotational symmetry typical for other bacteria.

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Держатели документа:
RAS, SB, Inst Computat Modelling, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Svobodny Prosp 79, Krasnoyarsk 660041, Russia.
VF Voino Yasenetsky Krasnoyarsk State Med Univ, P Zheleznjaka Str 1, Krasnoyarsk 660022, Russia.

Доп.точки доступа:
Sadovsky, Michael G.; Senashova, Maria Yu; Malyshev, Andrew V.