Naslov
Symbolic Cantor algorithm (SCA) : a method for the analysis of gene and protein coding

Autori
Štambuk, Nikola

Izvornik
Periodicum biologorum (0031-5362) 101 (1999), 4; 355-361

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
binary; gray code; SCA; horseshoe map; DNA; RNA; peptide; molecular recognition theory

Sažetak
Background and purpose: We define an alternative approach to Molecular Recognition Theory (MRT) and peptide/nucleotide complementary coding. The method is denoted Symbolic Cantor Algorithm (SCA) and represents an optimised procedure of the MRT based on the identification of the closest and most probable complementary amino acid ligands. SCA procedure is based on the Gray code solution of the DNA/RNA coding problem. Methods: By means of the Gray code analysis and binary tree projections of different codons/amino acids we show that RNA and DNA coding defines distinct groups of codon-anticodon pairs, which describe all possible complementary amino acid arrangements. This numerical result is statistically verified with the analysis of 9 different ligand-receptor systems and 32 tRNA gene transcripts. Results: Two fundamental properties of DNA/RNA, denoted as complementary and stationary coding are presented and analysed in the context of the nucleotide relationships of the same (self) and complementary (other or duplicated) strand. Two digit specification of the codon positions, by means of the binary group subdivision, is defined according to the purine-pyrimidine, amino-keto discrimination (clear binary text - noncoding genome regions) and purine-pyrimidine, strong-week H bonding discrimination (Gray code text - coding genome regions). The relations between binary tree locations and Cantor set representations of different codon points are defined with respect to the quadratic mappings, Smale's horseshoe map and symbolic dynamics. The metric distance (d) of symbol space is introduced and shown to define the codon projection dynamics within the standard genetic code table. This conversion enables the mapping of 64 six-dimensional hypercube nodes with binary addresses within 0 Ł d Ł 2 interval. Conclusion: SCA procedure may be a suitable method of defining codon addresses and metric distances for the linguistic analysis of DNA and RNA strings and related protein coding. The applications of this method may contribute to gene, protein and drug modelling.

Izvorni jezik
Engleski

Znanstvena područja
Temeljne medicinske znanosti

POVEZANOST RADA