[Text] : научное издание / Gorban A.N.,Zinovyev A.Y., Popova T. // Institut des Hautes Etudes Scientifiques Preprint . - 2001
Перевод заглавия: Статистический подход к автоматической идентификации генов без учителя
Аннотация: Overview of statistical methods of gene identification is made. Particular attention is given to the methods which need not a training set of already known genes. After analysis several statistical approaches are proposed for computational exon identification in whole genomes. For several genomes an optimal window length for averaging GC-content function and calculating codon frequencies has been found. Self-training procedure based on clustering in multidimensional codon frequencies space is proposed.
http://icm.krasn.ru/refextra.php?id=2108
Доп.точки доступа:
Zinovyev, A.Y.; Зиновьев, Андрей Юрьевич; Popova, T.G.; Попова Т.Г.; Горбань, Александр Николаевич
Труды сотрудников ИВМ СО РАН
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Statistical approaches to automated gene identification without teacher
A comprehensive modular map of molecular interactions in RB/E2F pathway
[Text] : статья / L. Calzone [et al.] // Molecular Systems Biology. - 2008. - Vol. 4. - p. 174-178DOI 10.1038/msb.2008.7
. -
Аннотация: We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large‐scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher‐level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Calzone, Laurence; Gelay, Amélie; Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Radvanyi, François; Barillot, Emmanuel
Аннотация: We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large‐scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher‐level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.
Держатели документа:
ИВМ СО РАН : 660036, Красноярск, Академгородок, 50, стр.44
Доп.точки доступа:
Calzone, Laurence; Gelay, Amélie; Zinovyev, Andrei; Зиновьев, Андрей Юрьевич; Radvanyi, François; Barillot, Emmanuel
THE COMPARATIVE REDUNDANCY OF GENES OF VARIOUS ORGANISMS AND VIRUSES
[Текст] / A. N. GORBAN [и др.] // Genetika. - 1993. - Vol. 29, Is. 9. - С. 1413-1419. - Cited References: 20
. - ISSN 0016-6758
РУБ Genetics & Heredity
Аннотация: This paper is devoted to the comparative stude of redundancy of genetic texts of various organisms and viruses. To determine the tedundance of a gene, we have introduced the strict measure for that latter. The measure for a text's redundance is the length of restriction of Frequence/Correlation Dictionary of a given genetic text. Frequence/Correlation Dictionary is the ser of all subsequences belang to a given genetic text, accompanied by the frequencies of their occurrence. The restriction length is defined as that one, for which all the subsequences (of that length) are unique. We have found, that genes of human viruses are less redundant, in comparison to those of human genes. Other aspects of a comparative redundance invastigations of the genes are discussed. The problem of the determination of <> intron could be treated by this methodology, as well, as the evolution of genome.
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Scopus
Держатели документа:
RUSSIAN ACAD SCI,CTR COMP,KRASNOYARSK,RUSSIA
ИВМ СО РАН
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Доп.точки доступа:
GORBAN, A.N.; Горбань, Александр Николаевич; MIRKES, E.M.; POPOVA, T.G.; SADOVSKY, M.G.; Садовский, Михаил Георгиевич
Рубрики:
CODON
Кл.слова (ненормированные):
article -- dna content -- evolution -- genome -- nonhuman -- restriction mapping -- virus -- amino acid sequence -- comparative study -- gene frequency -- human -- molecular genetics -- nucleotide sequence -- restriction mapping -- virus gene -- Amino Acid Sequence -- Base Sequence -- Comparative Study -- English Abstract -- Gene Frequency -- Genes, Viral -- Human -- Molecular Sequence Data -- Restriction Mapping
CODON
Кл.слова (ненормированные):
article -- dna content -- evolution -- genome -- nonhuman -- restriction mapping -- virus -- amino acid sequence -- comparative study -- gene frequency -- human -- molecular genetics -- nucleotide sequence -- restriction mapping -- virus gene -- Amino Acid Sequence -- Base Sequence -- Comparative Study -- English Abstract -- Gene Frequency -- Genes, Viral -- Human -- Molecular Sequence Data -- Restriction Mapping
Аннотация: This paper is devoted to the comparative stude of redundancy of genetic texts of various organisms and viruses. To determine the tedundance of a gene, we have introduced the strict measure for that latter. The measure for a text's redundance is the length of restriction of Frequence/Correlation Dictionary of a given genetic text. Frequence/Correlation Dictionary is the ser of all subsequences belang to a given genetic text, accompanied by the frequencies of their occurrence. The restriction length is defined as that one, for which all the subsequences (of that length) are unique. We have found, that genes of human viruses are less redundant, in comparison to those of human genes. Other aspects of a comparative redundance invastigations of the genes are discussed. The problem of the determination of <
WOS,
Scopus
Держатели документа:
RUSSIAN ACAD SCI,CTR COMP,KRASNOYARSK,RUSSIA
ИВМ СО РАН
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Доп.точки доступа:
GORBAN, A.N.; Горбань, Александр Николаевич; MIRKES, E.M.; POPOVA, T.G.; SADOVSKY, M.G.; Садовский, Михаил Георгиевич
Maximum entropy method in analysis of genetic text and measurement of its information content
/ N. N. Bugaenko, A. N. Gorban, M. G. Sadovsky // Open Systems and Information Dynamics. - 1998. - Vol. 5, Is. 3. - P265-278
. - ISSN 1230-1612
Аннотация: The information capacity in frequency dictionaries of nucleotide sequences is estimated through the efficiency of reconstruction of a longer frequency dictionary from a short one. This reconstruction is performed by the maximum entropy method. Real nucleotide sequences are compared to random ones (with the same composition of nucleotides). Phages genes from NCBI bank were analyzed. The reliable difference of real genetic texts from random sequences is observed for the dictionary length q = 2, 5 and 6.
Scopus
Держатели документа:
Computing Center, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russian Federation
ИВМ СО РАН
ИБФ СО РАН
Доп.точки доступа:
Bugaenko, N.N.; Gorban, A.N.; Горбань, Александр Николаевич; Sadovsky, M.G.; Садовский, Михаил Георгиевич
Аннотация: The information capacity in frequency dictionaries of nucleotide sequences is estimated through the efficiency of reconstruction of a longer frequency dictionary from a short one. This reconstruction is performed by the maximum entropy method. Real nucleotide sequences are compared to random ones (with the same composition of nucleotides). Phages genes from NCBI bank were analyzed. The reliable difference of real genetic texts from random sequences is observed for the dictionary length q = 2, 5 and 6.
Scopus
Держатели документа:
Computing Center, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russian Federation
ИВМ СО РАН
ИБФ СО РАН
Доп.точки доступа:
Bugaenko, N.N.; Gorban, A.N.; Горбань, Александр Николаевич; Sadovsky, M.G.; Садовский, Михаил Георгиевич
Strong inhomogeneity in triplet distribution alongside a genome
/ M. Sadovsky, X. Nikitina // (15 April 2015 through 17 April 2015. - 2015. - Vol. 9044. - P248-255
. -
Кл.слова (ненормированные):
Inhomogeneity -- Longest gap -- Order -- Periodicity -- Track -- Bioinformatics -- Biomedical engineering -- Mammals -- Inhomogeneities -- Longest gap -- Order -- Periodicity -- Track -- Genes
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.
Кл.слова (ненормированные):
Inhomogeneity -- Longest gap -- Order -- Periodicity -- Track -- Bioinformatics -- Biomedical engineering -- Mammals -- Inhomogeneities -- Longest gap -- Order -- Periodicity -- Track -- Genes
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.
Genome structure of organelles strongly relates to taxonomy of bearers
/ 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
. -
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Morphology -- Order -- Similitude -- Synchrony -- Triplet -- Bioinformatics -- Biology -- Biomedical engineering -- Morphology -- Taxonomies -- Cluster -- Evolution -- Frequency -- Order -- Similitude -- Synchrony -- Triplet -- Genes
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.
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Morphology -- Order -- Similitude -- Synchrony -- Triplet -- Bioinformatics -- Biology -- Biomedical engineering -- Morphology -- Taxonomies -- Cluster -- Evolution -- Frequency -- Order -- Similitude -- Synchrony -- Triplet -- Genes
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.
De novo assembly and cluster analysis of Siberian Larch transcriptome and genome
/ 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
. -
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Order -- Triplet -- Bioinformatics -- Biomedical engineering -- Genes -- Cluster -- Evolution -- Frequency -- Order -- Triplet -- Cluster analysis
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.
Кл.слова (ненормированные):
Cluster -- Elastic map -- Evolution -- Frequency -- Order -- Triplet -- Bioinformatics -- Biomedical engineering -- Genes -- Cluster -- Evolution -- Frequency -- Order -- Triplet -- Cluster analysis
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.
Scopus,
Смотреть статью,
WOS
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.
New error tolerant method for search of long repeats in DNA sequences
/ S. P. Tsarev, M. G. Sadovsky // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2016. - Vol. 9702: 3rd International Conference on Algorithms for Computational Biology, AlCoB 2016; Trujillo; Spain; 21 June 2016 through 22 June 2016; Code 177079. - P171-182, DOI 10.1007/978-3-319-38827-4_14
. -
Кл.слова (ненормированные):
Fast search -- Genome -- Vernier pattern -- Bioinformatics -- DNA -- Gages -- Genes -- Biological applications -- Error tolerant -- Fast search -- Search procedures -- Sparse dictionaries -- Sub-strings -- Vernier pattern -- DNA sequences
Аннотация: A new method to identify all sufficiently long repeating nucleotide substrings in one or several DNA sequences is proposed. The method based on a specific gauge applied to DNA sequences that guarantees identification of the repeating substrings. The method allows the matching substrings to contain a given level of errors. The gauge is based on the development of a heavily sparse dictionary of repeats, thus drastically accelerating the search procedure. Some biological applications illustrate the method. © Springer International Publishing Switzerland 2016.
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Держатели документа:
Siberian Federal University, Kirenskogo, 26, Krasnoyarsk, Russian Federation
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Tsarev, S. P.; Sadovsky, M. G.
Кл.слова (ненормированные):
Fast search -- Genome -- Vernier pattern -- Bioinformatics -- DNA -- Gages -- Genes -- Biological applications -- Error tolerant -- Fast search -- Search procedures -- Sparse dictionaries -- Sub-strings -- Vernier pattern -- DNA sequences
Аннотация: A new method to identify all sufficiently long repeating nucleotide substrings in one or several DNA sequences is proposed. The method based on a specific gauge applied to DNA sequences that guarantees identification of the repeating substrings. The method allows the matching substrings to contain a given level of errors. The gauge is based on the development of a heavily sparse dictionary of repeats, thus drastically accelerating the search procedure. Some biological applications illustrate the method. © Springer International Publishing Switzerland 2016.
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Держатели документа:
Siberian Federal University, Kirenskogo, 26, Krasnoyarsk, Russian Federation
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Доп.точки доступа:
Tsarev, S. P.; Sadovsky, M. G.
Lost strings in genomes: What sense do they make?
/ M. Sadovsky [et al.] // (26 April 2017 through 28 April 2017 : Springer Verlag, 2017. - Vol. 10209 LNCS. - P20-29, DOI 10.1007/978-3-319-56154-7_3
. -
Кл.слова (ненормированные):
Combinatorics -- Composition -- Diversity -- Evolution -- Order -- Selection -- Bioinformatics -- Biology -- Biomedical engineering -- Chemical analysis -- Combinatorics -- Diversity -- Evolution -- Order -- Selection -- Genes
Аннотация: We studied the sets of avoided strings to be observed over a family of genomes. It was found that the length of the minimal avoided string rarely exceeds 9 nucleotides, with neither respect to a phylogeny of a genome under consideration. The lists of the avoided strings observed over the sets of (related) genomes have been analyzed. Very low correlation between the phylogeny, and the set of those strings has been found. © Springer International Publishing AG 2017.
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Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Johannes Gutenberg-Universitat Mainz, Mainz, Germany
Institute of Space and Information Technologies, Siberian Federal University, Kirenskogo Str., 26, Krasnoyarsk, Russian Federation
Institute of Molecular Biology, Mainz, Germany
Доп.точки доступа:
Sadovsky, M.; Fontaine, J. -F.; Andrade-Navarro, M. A.; Yakubailik, Y.; Rudenko, N.
Кл.слова (ненормированные):
Combinatorics -- Composition -- Diversity -- Evolution -- Order -- Selection -- Bioinformatics -- Biology -- Biomedical engineering -- Chemical analysis -- Combinatorics -- Diversity -- Evolution -- Order -- Selection -- Genes
Аннотация: We studied the sets of avoided strings to be observed over a family of genomes. It was found that the length of the minimal avoided string rarely exceeds 9 nucleotides, with neither respect to a phylogeny of a genome under consideration. The lists of the avoided strings observed over the sets of (related) genomes have been analyzed. Very low correlation between the phylogeny, and the set of those strings has been found. © Springer International Publishing AG 2017.
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Держатели документа:
Institute of Computational Modelling of SB RAS, Akademgorodok, Krasnoyarsk, Russian Federation
Johannes Gutenberg-Universitat Mainz, Mainz, Germany
Institute of Space and Information Technologies, Siberian Federal University, Kirenskogo Str., 26, Krasnoyarsk, Russian Federation
Institute of Molecular Biology, Mainz, Germany
Доп.точки доступа:
Sadovsky, M.; Fontaine, J. -F.; Andrade-Navarro, M. A.; Yakubailik, Y.; Rudenko, N.
Chloroplast genomes exhibit eight-cluster structuredness and mirror symmetry
/ 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
. -
Кл.слова (ненормированные):
K-means -- Order -- Probability -- Projection -- Symmetry -- Triplet -- Bioinformatics -- Biomedical engineering -- Crystal symmetry -- Probability -- Chloroplast genome -- Frequency spaces -- K-means -- Mirror symmetry -- Order -- Projection -- Triplet -- Typical structures -- Genes
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.
Кл.слова (ненормированные):
K-means -- Order -- Probability -- Projection -- Symmetry -- Triplet -- Bioinformatics -- Biomedical engineering -- Crystal symmetry -- Probability -- Chloroplast genome -- Frequency spaces -- K-means -- Mirror symmetry -- Order -- Projection -- Triplet -- Typical structures -- Genes
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.
Function vs. Taxonomy: The Case of Fungi Mitochondria ATP Synthase Genes
/ 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
. -
Кл.слова (ненормированные):
Clustering -- Elastic map -- Evolution -- K-means -- Order -- Stability -- Bioinformatics -- Biomedical engineering -- Convergence of numerical methods -- Genes -- Mitochondria -- Taxonomies -- ATP synthase -- Clustering -- Evolution -- K-means -- Metric spaces -- Mitochondrial genomes -- Order -- K-means clustering
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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РИНЦ
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.
Кл.слова (ненормированные):
Clustering -- Elastic map -- Evolution -- K-means -- Order -- Stability -- Bioinformatics -- Biomedical engineering -- Convergence of numerical methods -- Genes -- Mitochondria -- Taxonomies -- ATP synthase -- Clustering -- Evolution -- K-means -- Metric spaces -- Mitochondrial genomes -- Order -- K-means clustering
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.
Scopus,
Смотреть статью,
РИНЦ
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.
Reads in NGS Are Distributed over a Sequence Very Inhomogeneously
/ M. Sadovsky [et al.] // (8 May 2019 through 10 May 2019 : Springer Verlag, 2019. - Vol. 11465 LNBI. - P271-282, DOI 10.1007/978-3-030-17938-0_25
. -
Кл.слова (ненормированные):
Digitalization -- Entropy -- Equilibrium -- Mutual entropy -- Order -- Bioinformatics -- Biomedical engineering -- Entropy -- Phase equilibria -- Bacterial genomes -- Digitalization -- Distribution patterns -- Inhomogeneities -- Kullback-Leibler distance -- Local density -- Mutual entropy -- Order -- Genes
Аннотация: Distribution of read starts over a sequences genetic entity is studied. Key question was whether the starts are distributed uniformly and homogeneously along a sequence, or there exist some spots of the increased local density of the starts. To answer the question, 15 bacterial genomes have been studied. It was found that some genomes exhibit extremely far distribution pattern, from an homogeneity, while others show lower level of the inhomogeneity. The inhomogeneity level was determined through the Kullback-Leibler distance between the real string distribution, and that one bearing the most probable continuations of the shorter strings. © 2019, Springer Nature Switzerland AG.
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РИНЦ
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
Institute of Space Research and Computer Sciences, Siberian Federal University, Kirenskogo str., 26, Krasnoyarsk, 660074, Russian Federation
Доп.точки доступа:
Sadovsky, M.; Kobets, V.; Khodos, G.; Kuzmin, D.; Sharov, V.
Кл.слова (ненормированные):
Digitalization -- Entropy -- Equilibrium -- Mutual entropy -- Order -- Bioinformatics -- Biomedical engineering -- Entropy -- Phase equilibria -- Bacterial genomes -- Digitalization -- Distribution patterns -- Inhomogeneities -- Kullback-Leibler distance -- Local density -- Mutual entropy -- Order -- Genes
Аннотация: Distribution of read starts over a sequences genetic entity is studied. Key question was whether the starts are distributed uniformly and homogeneously along a sequence, or there exist some spots of the increased local density of the starts. To answer the question, 15 bacterial genomes have been studied. It was found that some genomes exhibit extremely far distribution pattern, from an homogeneity, while others show lower level of the inhomogeneity. The inhomogeneity level was determined through the Kullback-Leibler distance between the real string distribution, and that one bearing the most probable continuations of the shorter strings. © 2019, Springer Nature Switzerland AG.
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РИНЦ
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
Institute of Space Research and Computer Sciences, Siberian Federal University, Kirenskogo str., 26, Krasnoyarsk, 660074, Russian Federation
Доп.точки доступа:
Sadovsky, M.; Kobets, V.; Khodos, G.; Kuzmin, D.; Sharov, V.
Non-Coding Regions of Chloroplast Genomes Exhibit a Structuredness of Five Types
/ 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
. -
Кл.слова (ненормированные):
Clustering -- Order -- Probability -- Projection -- Symmetry -- Triplet -- Bioinformatics -- Biomedical engineering -- Codes (symbols) -- Crystal symmetry -- Probability -- Chloroplast genome -- Clustering -- Euclidean spaces -- Non-coding region -- Order -- Projection -- Statistical properties -- Triplet -- Genes
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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Смотреть статью,
РИНЦ
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.
Кл.слова (ненормированные):
Clustering -- Order -- Probability -- Projection -- Symmetry -- Triplet -- Bioinformatics -- Biomedical engineering -- Codes (symbols) -- Crystal symmetry -- Probability -- Chloroplast genome -- Clustering -- Euclidean spaces -- Non-coding region -- Order -- Projection -- Statistical properties -- Triplet -- Genes
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.
Scopus,
Смотреть статью,
РИНЦ
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.
Amazing symmetrical clustering in chloroplast genomes
/ 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 1471-2105
РУБ 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.
WOS
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.
Рубрики:
PHYLOGENETIC ANALYSIS
DNA
EVOLUTION
SYSTEMATICS
MANIFOLDS
BACTERIA
Кл.слова (ненормированные):
Order -- Triplet -- Clustering
PHYLOGENETIC ANALYSIS
DNA
EVOLUTION
SYSTEMATICS
MANIFOLDS
BACTERIA
Кл.слова (ненормированные):
Order -- Triplet -- Clustering
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.
WOS
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.