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--- abstract: | Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the ``in-phase'' triplet distributions of relatively short genomic fragments (200-400bp). We found 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. We show that codon usage 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). All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/~zinovyev/7clusters The finding can be readily introduced into any software for gene prediction, sequence alignment or bacterial genomes classification. altloc: - http://mathcircle.org/gorban/ - http://www.ihes.fr/~zinovyev/ chapter: ~ commentary: ~ commref: ~ confdates: ~ conference: ~ confloc: ~ contact_email: ~ creators_id: [] creators_name: - family: Gorban given: A.N. honourific: '' lineage: '' - family: Popova given: T.G. honourific: '' lineage: '' - family: Zinovyev given: A.Yu. honourific: '' lineage: '' date: 2004-10 date_type: published datestamp: 2004-11-06 department: ~ dir: disk0/00/00/39/15 edit_lock_since: ~ edit_lock_until: ~ edit_lock_user: ~ editors_id: [] editors_name: [] eprint_status: archive eprintid: 3915 fileinfo: /style/images/fileicons/application_pdf.png;/3915/1/7clustersCog.pdf full_text_status: public importid: ~ institution: ~ isbn: ~ ispublished: ~ issn: ~ item_issues_comment: [] item_issues_count: 0 item_issues_description: [] item_issues_id: [] item_issues_reported_by: [] item_issues_resolved_by: [] item_issues_status: [] item_issues_timestamp: [] item_issues_type: [] keywords: 'codon usage, cluster structure, mean field, frequency dictionary' lastmod: 2011-03-11 08:55:43 latitude: ~ longitude: ~ metadata_visibility: show note: ~ number: ~ pagerange: ~ pubdom: FALSE publication: ~ publisher: ~ refereed: FALSE referencetext: | Audic S, Claverie JM. 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(2003). {\it Open Systems and Information Dynamics} {\bf 10}(4). p.321-333. relation_type: [] relation_uri: [] reportno: ~ rev_number: 12 series: ~ source: ~ status_changed: 2007-09-12 16:54:16 subjects: - bio-theory succeeds: ~ suggestions: ~ sword_depositor: ~ sword_slug: ~ thesistype: ~ title: |- Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences type: preprint userid: 4198 volume: ~