%0 Journal Article
%T Dinucleotide Circular Codes
%A Christian J. Michel
%A Giuseppe Pirillo
%J ISRN Biomathematics
%D 2013
%R 10.1155/2013/538631
%X We begin here a combinatorial study of dinucleotide circular codes. A word written on a circle is called circular. A set of dinucleotides is a circular code if all circular words constructed with this set have a unique decomposition. Propositions based on a letter necklace allow to determine the 24 maximum dinucleotide circular codes (of 6 elements). A partition property is also identified with eight self-complementary maximum dinucleotide circular codes and two classes of eight maximum dinucleotide circular codes in bijective correspondence by the complementarity map. 1. Introduction We continue our study of the combinatorial properties of circular codes in genes, that is, on the nucleotide alphabet . A dinucleotide is a word of two letters (diletter) on . A trinucleotide is a word of three letters (triletter) on . The two sets of 16 dinucleotides and 64 trinucleotides are codes in the sense of language theory but not circular codes [1, 2]. In order to have an intuitive meaning of these notions, codes are written on a straight line, while circular codes are written on a circle, but, in both cases, unique decipherability is required. Trinucleotide comma-free codes, a very particular case of trinucleotide circular codes, have been studied for a long time, see for example, [3¨C5]. After the discovery of a trinucleotide circular code in genes with strong mathematical properties [6], circular codes are mathematical objects studied in combinatorics, theoretical computer science, and theoretical biology. This theory underwent a rapid development, see for example, [7¨C27]. Trinucleotides are the fundamental words for genes, that is, the DNA sequences coding the amino acids constituting the protein sequences. However, dinucleotides are also words with important biological functions in genomes. Dinucleotides are involved in some genome sites, for example, the splice sites of introns in eukaryotic genomes are based on the dinucleotides and [28, 29]. Dinucleotides are also involved in some genome regions, for example, the dinucleotide in animal and plant genomes allows a positive or negative control over gene expression [30], and the dinucleotides [31, 32], [33], and [34] in eukaryotic genomes occur as concatenated words , (called tandem repeats in biology). We begin here a new combinatorial study concerning the dinucleotide circular codes. Their number, their list, and a partition according to the complementarity map are determined with propositions based on a letter necklace. 2. Preliminaries The following definitions and propositions are classical for any finite
%U http://www.hindawi.com/journals/isrn.biomathematics/2013/538631/