Treffer: Relational model of all genetic codes.

Title:
Relational model of all genetic codes.
Authors:
Štambuk N; Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia. Electronic address: nikolastambuk@gmail.com., Konjevoda P; Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia. Electronic address: pkonjev@irb.hr., Štambuk A; Faculty of Kinesiology, University of Zagreb, Horvaćanski zavoj 15, HR-10000, Zagreb, Croatia.
Source:
Bio Systems [Biosystems] 2025 Nov; Vol. 257, pp. 105600. Date of Electronic Publication: 2025 Sep 21.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Elsevier Science Ireland Country of Publication: Ireland NLM ID: 0430773 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1872-8324 (Electronic) Linking ISSN: 03032647 NLM ISO Abbreviation: Biosystems Subsets: MEDLINE
Imprint Name(s):
Publication: Limerick : Elsevier Science Ireland
Original Publication: Amsterdam, North-Holland Pub. Co.
MeSH Terms:
Genetic Code*/genetics , Models, Genetic*, Humans ; Codon/genetics
Contributed Indexing:
Keywords: Ambiguity; Codepoiesis; Evolution; First-order logic; Genetic codes; Relational model; Truth functions
Substance Nomenclature:
0 (Codon)
Entry Date(s):
Date Created: 20250923 Date Completed: 20251020 Latest Revision: 20251020
Update Code:
20251021
DOI:
10.1016/j.biosystems.2025.105600
PMID:
40987418
Database:
MEDLINE

Weitere Informationen

The most common way to display the rules of all genetic codes is the Standard Genetic Code (SGC) table and its variants. This article takes an alternative approach to the genetic code table based on the relational model (Konjevoda and Štambuk, 2021). The relational model (RM) proposes distributed storage of the data into a collection of tables, which are called relations. Basic elements of the SGC table are rows (called records or tuples) and columns (called attributes). The SGC table, according to the RM, represents the so-called unnormalized form of a table, and it can be decomposed or divided into 4 tables using a set of rules called normal forms. The rows and columns of a single table are defined by the first and second base, and individual tables are specified by the third codon base. The result of this model is an approach to managing genetic code data, represented in terms of tuples and grouped into relations, with table structure and language consistent with the first-order logic, and sixteen truth functions defined by IUPAC ambiguity codes for incomplete nucleic acid specification. It is concluded that the relational model is a suitable method to display the rules of the Standard Genetic Code and its 28 variants according to Marcello Barbieri's concepts of ambiguity reduction and codepoiesis.
(Copyright © 2025 Elsevier B.V. All rights reserved.)

Declaration of competing interest The authors declare no conflict of interest.