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Gorban, A. Codon usage trajectories and 7-cluster structure of 143 complete bacterial genornic sequences / A. . Gorban, T. . Popova, A. . Zinovyev> // Physica A. - 2005. - Vol. 353. - P. 365-387, DOI 10.1016/j.physa.2005.01.043. - Cited References: 46
. - ISSN 0378-4371РУБ Physics, Multidisciplinary Рубрики: DNA-BASE COMPOSITION ASYMMETRIC SUBSTITUTION PATTERNS PROTEIN-CODING REGIONS MICROBIAL GENOMES GENE IDENTIFICATION MARKOV-MODELS G+C CONTENT BIAS PREDICTION SELECTION Кл.слова (ненормированные): genome -- cluster -- codon usage -- correlations -- entropy -- mean field -- Cluster -- Codon usage -- Correlations -- Entropy -- Genome -- Mean field -- Approximation theory -- Correlation methods -- Database systems -- Entropy -- Functions -- Genes -- Mathematical models -- Clusters -- Codon usage -- Genomes -- Mean field -- Bacteria Аннотация: Three results are presented. First, we prove the existence of a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties. The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic "pure" types of this model, observed in nature: "parallel triangles", "perpendicular triangles", degenerated case and the flower-like type. Second, we answered the question: how big are the position-specific information and the contribution connected with correlations between nucleotide. The accuracy of the mean-field (context-free) approximation is estimated for bacterial genomes. We show that codon us-age of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea). Description of these two codon-usage trajectories is the third result. All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/similar to zinovyev/7clusters. (c) 2005 Elsevier B.V. All rights reserved.
WOS, Scopus, Читать в сети ИФ Держатели документа: Univ Leicester, Dept Math, Leicester LE1 7RH, Leics, England RAS, SB, Inst Computat Modelling, Krasnoyarsk, Russia Bures Sur Yvette & Bioinformat Serv Inst Curie, Inst Hautes Etudes Sci, Paris, France ИВМ СО РАН Department of Mathematics, University of Leicester, Leicester, University Road, Leicester LE1 7RH, United Kingdom Institute of Computational Modelling, SB RAS, Krasnoyarsk, Russian Federation Institut des Hautes Etudes Scientifiques, Bures-sur-Yvette and Bioinformatics Service of Institut Curie, Paris, France Доп.точки доступа: Popova, T.; Zinovyev, A. } Найти похожие
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