title: Circular codes, symmetries and transformations.
abstract: Circular codes, putative remnants of primeval comma-free codes, have gained considerable attention in the last years. In fact they represent a second kind of genetic code potentially involved in detecting and maintaining the normal reading frame in protein coding sequences. The discovering of an universal code across species suggested many theoretical and experimental questions. However, there is a key aspect that relates circular codes to symmetries and transformations that remains to a large extent unexplored. In this article we aim at addressing the issue by studying the symmetries and transformations that connect different circular codes. The main result is that the class of 216 C3 maximal self-complementary codes can be partitioned into 27 equivalence classes defined by a particular set of transformations. We show that such transformations can be put in a group theoretic framework with an intuitive geometric interpretation. More general mathematical results about symmetry transformations which are valid for any kind of circular codes are also presented. Our results pave the way to the study of the biological consequences of the mathematical structure behind circular codes and contribute to shed light on the evolutionary steps that led to the observed symmetries of present codes.
authors.affiliation: Faculty of Computer Sciences, Institute of Applied Mathematics, Mannheim University of Applied Sciences, 68163 , Mannheim, Germany, e.fimmel@hs-mannheim.de.
authors.forename: Elena
authors.initials: E
authors.lastname: Fimmel
authors.forename: Simone
authors.initials: S
authors.lastname: Giannerini
authors.forename: Diego Luis
authors.initials: DL
authors.lastname: Gonzalez
authors.forename: Lutz
authors.initials: L
authors.lastname: Strüngmann
mesh_terms: D003062:Codon; D019143:Evolution, Molecular; D005815:Genetic Code; D055641:Mathematical Concepts; D008957:Models, Genetic; D014176:Protein Biosynthesis; D016364:Reading Frames
chemical_list: D003062:Codon