Diletter circular codes over finite alphabets

被引：11

作者：

Fimmel, Elena ^{[1
]}

Michel, Christian J. ^{[2
]}

Struengrnann, Lutz ^{[1
]}

机构：

[1] Univ Appl Sci, Fac Comp Sci, Inst Math Biol, D-68163 Mannheim, Germany

[2] Univ Strasbourg, CNRS, Theoret Bioinformat, 300 Blvd Sebastien Brant, F-67400 Illkirch Graffenstaden, France

来源：

MATHEMATICAL BIOSCIENCES | 2017年 / 294卷

关键词：

Diletter circular code; Finite alphabet; Enumerative combinatorics; COMMA-FREE CODES; MAXIMAL DINUCLEOTIDE; DNA-SEQUENCES; PROTEIN; EVOLUTION; MOTIFS; GENES; EUKARYOTES; REGIONS;

D O I：

10.1016/j.mbs.2017.10.001

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The graph approach of circular codes recently developed (Fimmel et al., 2016) allows here a detailed study of diletter circular codes over finite alphabets. A new class of circular codes is identified, strong comma-free codes. New theorems are proved with the diletter circular codes of maximal length in relation to (i) a characterisation of their graphs as acyclic tournaments; (ii) their explicit description; and (iii) the non-existence of other maximal diletter circular codes. The maximal lengths of paths in the graphs of the comma-free and strong comma-free codes are determined. Furthermore, for the first time, diletter circular codes are enumerated over finite alphabets. Biological consequences of dinucleotide circular codes are analysed with respect to their embedding in the trinucleotide circular code X identified in genes and to the periodicity modulo 2 observed in introns. An evolutionary hypothesis of circular codes is also proposed according to their combinatorial properties.

引用

页码：120 / 129

页数：10

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