Труды сотрудников ИВМ СО РАН

[Текст] : статья / Е.Ю. Бушмелев и др. // 8-th European conf. on Mathematical and Theoretical Biology. - 2011. - p. 78


Доп.точки доступа:
Садовский, Михаил Георгиевич; Sadovskii M.G.

[Текст] : статья / Е.Ю. Бушмелев и др. // Int. conf. on Bioinformatics. - 2011. - p. 65


Доп.точки доступа:
Садовский, Михаил Георгиевич; Sadovskii M.G.

[Текст] / E. M. Mirkes, M. G. Sadovsky // Proc. IWBBIO-2013. - 2013. - С. 89-97

Полный текст на сайте конференции


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

/ M. Sadovsky, X. Nikitina // (15 April 2015 through 17 April 2015. - 2015. - Vol. 9044. - P248-255 . -
Аннотация: The distribution of triplets alongside a genome is studied.We explored the distribution to the nearest neighbour, that is the pattern where two triplets are fixed, and the distance is determined from the former to the latter so that the second triplet takes place nowhere inside the observed gap surrounded with the couple of the given triplets. The distribution differs strongly, for different organisms. Yeast and bacteria seem to have rather smooth pattern, while mammalia and other higher eukaryotes exhibit very complex patterns with long-range correlations in the triplet distribution. © Springer International Publishing Switzerland 2015.

Scopus

Держатели документа:
Institute of computational modelling of SB RASAkademgorodok, Krasnoyarsk, Russian Federation
ИВМ СО РАН

Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Nikitina, X.

/ M. Sadovsky [et al.] // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2015. - Vol. 9043: 3rd International Work Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015; Granada; Spain; 15 April 2015 through 17 April 2015; Code 125929. - P481-490 . -
Аннотация: We studied the relations between the triplet frequency dictionaries of organelle genome, and the phylogeny of their bearers. The clusters in 63-dimensional space were identified through K-means, and the clade composition of those clusters has been investigated. Very high regularity in genomes distribution among the clusters was found, in terms of taxonomy. The strong synchrony in evolution of nuclear and organelle genomes manifests through this correlation: the proximity in frequency space was determined over the organelle genomes, while the proximity in taxonomy was determined morphologically. Similar effect is also found in the ensembles of other (say, yeast) genomes. © Springer International Publishing Switzerland 2015.

Scopus

Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Putintseva, Y.; Chernyshova, A.; Fedotova, V.

[Text] : статья / Michael G. Sadovsky [et al.] // Журнал Сибирского федерального университета. Серия: Биология. - 2015. - Т. 8, № 3. - P278-286, DOI 10.17516/1997-1389-2015-8-3-278-286 . - ISSN 1997-1389
   Перевод заглавия: Симметрия транскриптома сибирской лиственницы

УДК

57

015 + 573.2

Аннотация: The paper presents a novel approach to infer a structuredness in a set of symbol sequences such as transcriptome nucleotide sequences. A distribution pattern of triplet frequencies in the Siberian larch (Larix sibirica Ledeb.) transcriptome sequences was investigated in the presented study. It was found that the larch transcriptome demonstrates a number of unexpected symmetries in the statistical and combinatorial properties.
Проанализированы структуры, выделяемые в транскриптоме лиственницы. Показано, что данный набор последовательностей обладает необычной симметрией своих статистических и комбинаторных свойств.

РИНЦ

Держатели документа:
Georg-August-University of Gottingen
Institute of Computational Modelling SB RAS
M University HFSB
N. I. Vavilov Institute of General Genetics RAS
Siberian Federal University Genome Research and Education Centre
Texas A&amp
V. N. Sukachev Institute of Forest SB RAS

Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Birukov, Vladislav V.; Бирюков В.В.; Putintseva, Yuliya A.; Путинцева Ю.А.; Oreshkova, Nataliya V.; Орешкова Н.В.; Vaganov, Eugene A.; Ваганов Е.А.; Krutovsky, Konstantin V.; Крутовский К.В.

[Text] : статья / M. G. Sadovsky [et al.] // Журнал Сибирского федерального университета. Серия: Биология. - 2015. - Т. 8, № 3. - P268-277, DOI 10.17516/1997-1389-2015-8-3-268-277. . - ISSN 1997-1389
   Перевод заглавия: Семикластерная структура генома хлоропласта лиственницы

УДК

57

015 + 573.2

Аннотация: The paper presents a novel approach to study a nucleotide sequence structure with respect to the chloroplast genome DNA sequence analysis. A speci?c frequencies distribution pattern of the consecutive triple nucleotide fragments was identi?ed in the chloroplast genome DNA sequence, which demonstrated a non-degenerated pattern with seven clusters.
Проанализированы структуры, выделяемые в нуклеотидных последовательностях с помощью анализа распределений фрагментов генома. Показано, что последовательность генома хлоропласта обладает невырожденной семикластерной структурой в распределении таких фрагментов по частотам триплетов.

РИНЦ

Держатели документа:
Georg-August-University of Gottingen
Institute of Computational Modelling SB RAS
M University HFSB
N. I. Vavilov Institute of General Genetics RAS
Siberian Federal University Genome Research and Education Centre
Texas A&amp
V. N. Sukachev Institute of Forest SB RAS

Доп.точки доступа:
Sadovsky, M.G.; Садовский, Михаил Георгиевич; Bondar, Eugenia I.; Бондар Е.И.; Putintseva, Yulia A.; Путинцева Ю.А.; Oreshkova, Natalia V.; Орешкова Н.В.; Vaganov, Eugene A.; Ваганов Е.А.; Krutovsky, Konstantin V.; Крутовский К.В.

/ M. Sadovsky [et al.] // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2016. - Vol. 9656: 4th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016; Granada; Spain; 20 April 2016 through 22 April 2016; Code 173369. - P455-464, DOI 10.1007/978-3-319-31744-1_41 . -
Аннотация: We studied Siberian Larch (Larix Sibirica) transcriptome making de novo assembly and cluster analysis of contigs frequency dictionaries. Also, some preliminary results of similar study of the larch genome are present. It was found that the larch transcriptome yields a number of unexpected symmetries in the statistical and combinatorial properties of the entities. © Springer International Publishing Switzerland 2016.

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Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Sadovsky, M.; Putintseva, Y.; Birukov, V.; Novikova, S.; Krutovsky, K.

[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

[Текст] : научное издание / М. Ю. Сенашова, М. Г. Садовский // Международный журнал прикладных и фундаментальных исследований. - 2016. - № 12-7. - С. 1167-1173 . - ISSN 1996-3955
   Перевод заглавия: 7-cluster pattern of chloroplast genomes correlates to phylogeny of their bearers

УДК

573.22

575.89

Аннотация: Представлены предварительные результаты исследования структуры геномов хлоропластов. Под структурой понимается кластеризация точек, соответствующих отдельным фрагментам генома хлоропласта (длиной порядка 200 нуклеотидов) в пространстве частот триплетов; частоты триплетов подсчитывались с пересечением, так, что каждый нуклеотид давал старт триплету. Было проанализировано 188 геномов хлоропластов растений самых разных таксономических уровней. Геном хлоропластов преобразовывался в частотные словари триплетов. Затем для каждого генома в 63-мерном пространстве этих частот при помощи программы VidaExpert были построены проекции данных, соответствующих выделяемым фрагментам генома, в пространстве первых трёх главных компонент. Было обнаружено, что подавляющее большинство геномов в пространстве первых трёх главных компонент имеет очень похожую пространственную структуру. Кроме того, для геномов вычислялся CG-контент, который является ведущим параметром классификации семикластерных структур геномов бактерий; ожидалось, что хлоропласты, ведущие своё происхождение от бактерий, будут также подчиняться этому правилу. Было установлено, что для хлоропластов данный параметр не является ведущим в классификации структур, наблюдаемых при анализе главных компонент распределения фрагментов геномов в пространстве частот триплетов.
Some preliminary results on the chloroplast genomes structure are provided. Structure here is an order observed within a set of points in 63-dimenstional metric space, where each point is the frequency dictionary of a fragment of a chromosome of the length app. 200 nucleotides; the fragments are identified with a step in 10 nucleotides. Frequency dictionary contains all triplets (with on exception), and the triplets have been counted so that these latter intersected, and each nucleotide gives a start for a triplet. Thus, about 15 000 fragments were identified, and converted into the points. The triplet yielding the least standard deviation over the set of the points has been eliminated. 188 chloroplast genomes of plants of various taxonomy were analyzed. Cluster stricture of the set of the points was elaborated with ViDaExpert software. It was found the genomes exhibit rather similar seven-cluster structure, especially apparent in principal component space; alongside the clusterisation, GC-content has been counted, for each genome, since it is suspected to be the key factor in pattern regulation. Unlike for bacterial genomes, GC-content was not found to be the key factor.

РИНЦ

Держатели документа:
ФГБУН «Федеральный исследовательский центр «Красноярский научный центр Сибирского отделения Российской академии наук»» — обособленное подразделение «Институт вычислительного моделирования Сибирского отделения Российской академии наук»

Доп.точки доступа:
Сенашова, М. Ю.; Senashova M. Yu.; Садовский, М. Г.; Sadovskiy M. G.

[Текст] : статья / М. Ю. Сенашова, М. Г. Садовский // Международный журнал прикладных и фундаментальных исследований. - 2017. - № 11-2. - С. 255-259 . - ISSN 1996-3955
   Перевод заглавия: Spatial structure of genomes of cyanobacteria

УДК

573.22

575.89

Аннотация: Представлены результаты, полученные при изучении пространственной структуры геномов цианобактерий. В качестве структуры в нашей работе понимается расположение в пространстве частот триплетов точек, соответствующих выделенным участкам генома цианобактерий. Для каждого участка длины ? со сдвигом t вычислялся частотный словарь троек символов без пересечений. Частоты рассматривались как координаты в 64-мерном пространстве. Таким образом, каждому участку генома сопоставлялась точка в пространстве частот. Было проанализировано 7 геномов цианобактерий, размещенных в EMBL-банке. Одна координата (с минимальным стандартным отклонением) отбрасывалась и в дальнейшем рассматривалось 63-мерное пространство частот. Для визуализации полученного множества точек была использована программа VidaExpert. С ее помощью для каждого генома были построены проекции в пространство первых трёх главных компонент из 63-мерного пространства частот. Мы обнаружили, что геномы цианобактерий обладают одинаковой структурой, представляющей собой своеобразный клубок из нитей. Причем нити образованы точками, соответствующими последовательным участкам генома.
The results obtained in the study of the structure of the genomes of cyanobacteria are presented. By structure in our work is meant the location in space of triplet frequencies of points corresponding to fragments of the genome of cyanobacteria. For each length-shifted fragments, a frequency dictionary of symbol triples without intersections was computed. Frequencies were considered as coordinates in a 64-dimensional space. Thus, each point of the genome was compared with a point in the frequency space. Seven genomes of cyanobacteria located in the EMBL-bank were analyzed. One coordinate (with a minimal standard deviation) was discarded and a 63-dimensional frequency space was subsequently considered. For each genome in space of frequencies by means of program VidaExpert projections from 63-dimensional space in space of first three main components have been constructed. This allowed us to visualize the structure of genomes. It was found that the genomes of cyanobacteria have the same structure, which is a kind of tangle of filaments. And the threads are formed by points corresponding to consecutive fragments of the genome.

РИНЦ

Держатели документа:
ФГАОУ «Сибирский федеральный университет», институт фундаментальной биологии и биотехнологии
ФГБУН «Федеральный исследовательский центр “Красноярский научный центр Сибирского отделения Российской академии наук”» - обособленное подразделение «Институт вычислительного моделирования» Сибирского отделения Российской академии наук»

Доп.точки доступа:
Сенашова, М.Ю.; Senashova M.Yu.; Садовский, М.Г.; Sadovskiy M.G.

[Текст] : статья / М. Г. Садовский, М. Ю. Сенашова, А. В. Малышев // Журнал общей биологии. - 2018. - Т. 79, № 2. - С. 124-134 . - ISSN 0044-4596
   Перевод заглавия: Eight-cluster genome structure in chloroplasts of terrestrial plants

УДК	57.015 + 573.2

Аннотация: В данной работе было проверено, является ли семикластерная структура, обнаруженная у бактерий, универсальной и наблюдаются ли все обнаруженные свойства такой структуры для других геномов. Исследована внутренняя структурированность геномов хлоропластов и цианобактерий, показано, что эта структурированность существенно отличается от ранее обнаруженной для бактериальных геномов. Под структурированностью понимается кластеризация частотных словарей триплетов отдельных фрагментов генома, определяемых регулярным порядком, вне зависимости от функциональной роли того или иного участка. Кластеризация проводилась методом упругих карт.
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 cyano-bacteria'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.

РИНЦ

Держатели документа:
Институт вычислительного моделирования СО РАН
Сибирский Федеральный университет Институт фундаментальной биологии и биотехнологии

Доп.точки доступа:
Садовский, М.Г.; Sadovsky M.G.; Сенашова, М.Ю.; Senashova M. Yu.; Малышев, А.В.; Malyshev A.V.

/ M. Sadovsky, M. Senashova, A. Malyshev // (25 April 2018 through 27 April 2018 : Springer Verlag, 2018. - Vol. 10813 LNBI. - P186-196, DOI 10.1007/978-3-319-78723-7_16 . -
Аннотация: Chloroplast genomes have eight-cluster structuredness, in triplet frequency space. Small fragments of a genome converted into a triplet frequency dictionaries are the elements to be clustered. Typical structure consists of eight clusters: six of them correspond to three different positions of a reading frame shifted for 0, 1 and 2 nucleotides (in two opposing strands), the seventh cluster corresponds to a junk regions of a genome, and the eighth cluster is comprised by the fragments with excessive GC-content bearing specific RNA genes. The structure exhibits a specific symmetry. © 2018, Springer International Publishing AG, part of Springer Nature.

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Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodny Prospect, 79, Krasnoyarsk, Russian Federation

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

/ 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, Y. A. Putintseva // : Nova Science Publishers, Inc., 2018. - P25-96 . -
Аннотация: We studied the features and characters of various chloroplast genomes that could be retrieved solely from the analysis of triplet composition. To do that, two types of triplet dictionaries were developed: the former lists all the triplets (with overlapping), so that each nucleotide yields a start for a triplet, and the latter is the entity where triplets do not overlap, but also have no gaps between them. Two main cores were studied: the former is the structuredness of a genome that manifests in the statistical properties of small fragments of the genome, each of them converted into a triplet frequency dictionary, and the latter is the relation between the triplet frequencies of a genome, and their phylogeny, when determined over a significant ensemble of genomes. It was found that the great majority of chloroplast genomes exhibit a specific eight-cluster pattern comprising these fragments (converted into triplet frequency dictionaries). The first cluster corresponds to junk fragments, and six more clusters correspond to the fragments corresponding to coding regions, so that each entity corresponds to the specific reading frame shift, and the strand (leading vs. ladder). Finally, the eighth cluster (called the "tail") differs from all those mentioned above, and comprises the fragments with excessive GC-content values. In the observed pattern, two clusters corresponding to the third position of a reading frame but belonging to opposite strands always project one over the other, while the other four clusters do not. Moreover, there is a mirroring symmetry in the orientation of these two coincidental clusters against four others: each genome has either left-hand or right-hand orientation of these six clusters. The cluster structuredness of the chloroplasts found here differs from a similar one observed for bacterial or eukaryotic genomes. The aim of the second core investigation was to establish the relation between the triplet composition of chloroplast genomes and the taxonomy of their bearers; the latter was determined morphologically, by nuclear genomes. To reveal the relation, all the chloroplast genomes (approx. 900 entries) were converted into triplet frequency dictionaries of the first type, and then they were clustered by K-means, elastic maps and some other clustering techniques into two, three, four, five, six and seven classes, respectively. The composition of the classes was the subject of interest: it was found that the distribution of clades over the classes that developed due to clustering was very non-random, and followed, in general, a natural taxonomy of the bearers. Some further perspectives and problems are discussed. © 2018 Nova Science Publishers, Inc. All rights reserved.

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Держатели документа:
Institute of Computational Modeling, SB RAS, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Sadovsky, M. G.; Senashova, M. Y.; Putintseva, Y. A.

/ M. Sadovsky [et al.] // (8 May 2019 through 10 May 2019 : Springer Verlag, 2019. - Vol. 11465 LNBI. - P335-345, DOI 10.1007/978-3-030-17938-0_30 . -
Аннотация: We studied the relations between triplet composition of the family of mitochondrial atp6, atp8 and atp9 genes, their function, and taxonomy of the bearers. The points in 64-dimensional metric space corresponding to genes have been clustered. It was found the points are separated into three clusters corresponding to those genes. 223 mitochondrial genomes have been enrolled into the database. © 2019, Springer Nature Switzerland AG.

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Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodny prosp., 79, Krasnoyarsk, 660049, Russian Federation
Laboratory of Genomics and Biotechnology, Federal Research Center RAS, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Sadovsky, M.; Fedotovskaya, V.; Kolesnikova, A.; Shpagina, T.; Putintseva, Y.

/ M. Sadovsky, T. Guseva, V. Biriukov // (8 May 2019 through 10 May 2019 : Springer Verlag, 2019. - Vol. 11465 LNBI. - P370-378, DOI 10.1007/978-3-030-17938-0_33 . -
Аннотация: We studied the structuredness inA total transcriptome of Siberian larch. To do that, the contigs from total transcriptome has been labeled with the reads comprising the tissue specific transcriptomes, and the distribution of the contigs from the total transcriptome has been developed with respect to the mutual entropy of the frequencies of occurrence of reads from tissue specific transcriptomes. It was found that a number of contigs contain comparable amounts of reads from different tissues, so the chimeric transcripts to be extremely abundant. On the contrary, the transcripts with high tissue specificity do not yield a reliable clustering revealing the tissue specificity. This fact makes usage of total transcriptome for the purposes of differential expression arguable. © 2019, Springer Nature Switzerland AG.

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Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk 660036, Russian Federation
Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodny prosp., 79, Krasnoyarsk, 660049, Russian Federation

Доп.точки доступа:
Sadovsky, M.; Guseva, T.; Biriukov, V.

/ M. Sadovsky [et al.] // (8 May 2019 through 10 May 2019 : Springer Verlag, 2019. - Vol. 11465 LNBI. - P346-355, DOI 10.1007/978-3-030-17938-0_31 . -
Аннотация: We studied the statistical properties of non-coding regions of chloroplast genomes of 391 plants. To do that, each non-coding region has been tiled with a set of overlapping fragments of the same length, and those fragments were transformed into triplet frequency dictionaries. The dictionaries were clustered in 64-dimensional Euclidean space. Five types of the distributions were identified: ball, ball with tail, ball with two tails, lens with tail, and lens with two tails. Besides, the multi-genome distribution has been studied: there are ten species performing an isolated and distant cluster; surprisingly, there is no immediate and simple relation in taxonomy composition of these clusters. © 2019, Springer Nature Switzerland AG.

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Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk 660036, Russian Federation
Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodny prosp., 79, Krasnoyarsk, 660049, Russian Federation

Доп.точки доступа:
Sadovsky, M.; Senashova, M.; Gorban, I.; Gustov, V.

[Text] / M. G. Sadovsky, M. Y. Senashova, Y. A. Putintseva // Chloroplasts and Cytoplasm: Structure and Functions : Nova Science Publishers, Inc., 2018. - P25-96
Аннотация: We studied the features and characters of various chloroplast genomes that could be retrieved solely from the analysis of triplet composition. To do that, two types of triplet dictionaries were developed: the former lists all the triplets (with overlapping), so that each nucleotide yields a start for a triplet, and the latter is the entity where triplets do not overlap, but also have no gaps between them. Two main cores were studied: the former is the structuredness of a genome that manifests in the statistical properties of small fragments of the genome, each of them converted into a triplet frequency dictionary, and the latter is the relation between the triplet frequencies of a genome, and their phylogeny, when determined over a significant ensemble of genomes. It was found that the great majority of chloroplast genomes exhibit a specific eight-cluster pattern comprising these fragments (converted into triplet frequency dictionaries). The first cluster corresponds to junk fragments, and six more clusters correspond to the fragments corresponding to coding regions, so that each entity corresponds to the specific reading frame shift, and the strand (leading vs. ladder). Finally, the eighth cluster (called the "tail") differs from all those mentioned above, and comprises the fragments with excessive GC-content values. In the observed pattern, two clusters corresponding to the third position of a reading frame but belonging to opposite strands always project one over the other, while the other four clusters do not. Moreover, there is a mirroring symmetry in the orientation of these two coincidental clusters against four others: each genome has either left-hand or right-hand orientation of these six clusters. The cluster structuredness of the chloroplasts found here differs from a similar one observed for bacterial or eukaryotic genomes. The aim of the second core investigation was to establish the relation between the triplet composition of chloroplast genomes and the taxonomy of their bearers; the latter was determined morphologically, by nuclear genomes. To reveal the relation, all the chloroplast genomes (approx. 900 entries) were converted into triplet frequency dictionaries of the first type, and then they were clustered by K-means, elastic maps and some other clustering techniques into two, three, four, five, six and seven classes, respectively. The composition of the classes was the subject of interest: it was found that the distribution of clades over the classes that developed due to clustering was very non-random, and followed, in general, a natural taxonomy of the bearers. Some further perspectives and problems are discussed.

РИНЦ,
Источник статьи

Держатели документа:
Institute of Computational Modeling|SB RAS
Siberian Federal University

Доп.точки доступа:
Sadovsky, M.G.; Senashova, M.Y.; Putintseva, Y.A.
Нет сведений об экземплярах (Источник в БД не найден)

[Text] / M. G. Sadovsky, M. Y. Senashova, Y. A. Putintseva // Chloroplasts and Cytoplasm: Structure and Functions : Nova Science Publishers, Inc., 2018. - P25-96
Аннотация: We studied the features and characters of various chloroplast genomes that could be retrieved solely from the analysis of triplet composition. To do that, two types of triplet dictionaries were developed: the former lists all the triplets (with overlapping), so that each nucleotide yields a start for a triplet, and the latter is the entity where triplets do not overlap, but also have no gaps between them. Two main cores were studied: the former is the structuredness of a genome that manifests in the statistical properties of small fragments of the genome, each of them converted into a triplet frequency dictionary, and the latter is the relation between the triplet frequencies of a genome, and their phylogeny, when determined over a significant ensemble of genomes. It was found that the great majority of chloroplast genomes exhibit a specific eight-cluster pattern comprising these fragments (converted into triplet frequency dictionaries). The first cluster corresponds to junk fragments, and six more clusters correspond to the fragments corresponding to coding regions, so that each entity corresponds to the specific reading frame shift, and the strand (leading vs. ladder). Finally, the eighth cluster (called the "tail") differs from all those mentioned above, and comprises the fragments with excessive GC-content values. In the observed pattern, two clusters corresponding to the third position of a reading frame but belonging to opposite strands always project one over the other, while the other four clusters do not. Moreover, there is a mirroring symmetry in the orientation of these two coincidental clusters against four others: each genome has either left-hand or right-hand orientation of these six clusters. The cluster structuredness of the chloroplasts found here differs from a similar one observed for bacterial or eukaryotic genomes. The aim of the second core investigation was to establish the relation between the triplet composition of chloroplast genomes and the taxonomy of their bearers; the latter was determined morphologically, by nuclear genomes. To reveal the relation, all the chloroplast genomes (approx. 900 entries) were converted into triplet frequency dictionaries of the first type, and then they were clustered by K-means, elastic maps and some other clustering techniques into two, three, four, five, six and seven classes, respectively. The composition of the classes was the subject of interest: it was found that the distribution of clades over the classes that developed due to clustering was very non-random, and followed, in general, a natural taxonomy of the bearers. Some further perspectives and problems are discussed.

РИНЦ,
Источник статьи

Держатели документа:
Institute of Computational Modeling|SB RAS
Siberian Federal University

Доп.точки доступа:
Sadovsky, M.G.; Senashova, M.Y.; Putintseva, Y.A.
Нет сведений об экземплярах (Источник в БД не найден)