title: Maximal dinucleotide comma-free codes.
abstract: The problem of retrieval and maintenance of the correct reading frame plays a significant role in RNA transcription. Circular codes, and especially comma-free codes, can help to understand the underlying mechanisms of error-detection in this process. In recent years much attention has been paid to the investigation of trinucleotide circular codes (see, for instance, Fimmel et al., 2014; Fimmel and Strüngmann, 2015a; Michel and Pirillo, 2012; Michel et al., 2012, 2008), while dinucleotide codes had been touched on only marginally, even though dinucleotides are associated to important biological functions. Recently, all maximal dinucleotide circular codes were classified (Fimmel et al., 2015; Michel and Pirillo, 2013). The present paper studies maximal dinucleotide comma-free codes and their close connection to maximal dinucleotide circular codes. We give a construction principle for such codes and provide a graphical representation that allows them to be visualized geometrically. Moreover, we compare the results for dinucleotide codes with the corresponding situation for trinucleotide maximal self-complementary C(3)-codes. Finally, the results obtained are discussed with respect to Crick׳s hypothesis about frame-shift-detecting codes without commas.
authors.affiliation: Institute of Mathematical Biology, Faculty of Computer Sciences, Mannheim University of Applied Sciences, 68163 Mannheim, Germany. Electronic address: e.fimmel@hs-mannheim.de.
authors.forename: Elena
authors.initials: E
authors.lastname: Fimmel
authors.affiliation: Institute of Mathematical Biology, Faculty of Computer Sciences, Mannheim University of Applied Sciences, 68163 Mannheim, Germany. Electronic address: l.struengmann@hs-mannheim.de.
authors.forename: Lutz
authors.initials: L
authors.lastname: Strüngmann
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D003062:Codon; D003196:Computer Graphics; D003198:Computer Simulation; D019143:Evolution, Molecular; D005815:Genetic Code; D016678:Genome; D008957:Models, Genetic; D009711:Nucleotides / Q000737:chemistry* / Q000235:genetics; D012313:RNA / Q000235:genetics; D015203:Reproducibility of Results; D014158:Transcription, Genetic
chemical_list: D000596:Amino Acids; D003062:Codon; D009711:Nucleotides; D012313:RNA
keywords: Circular code; Comma-free code; Dinucleotides; Genetic code