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/ 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.

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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] / 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, 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.

[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.

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

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

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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,
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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,
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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,
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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)