title: Circular code motifs in transfer RNAs.
abstract: In 1996, a trinucleotide circular code X is identified in genes of prokaryotes and eukaryotes (Arquès and Michel, 1996). In 2012, X motifs are identified in the transfer RNA (tRNA) Phe and 16S ribosomal RNA (Michel, 2012). A statistical analysis of X motifs in all available tRNAs of prokaryotes and eukaryotes in the genomic tRNA database (September 2012, http://lowelab.ucsc.edu/GtRNAdb/, Lowe and Eddy, 1997) is carried out here. For this purpose, a search algorithm of X motifs in a DNA sequence is developed. Two definitions allow to determine the occurrence probabilities of X motifs and the circular codes X, X1=P(X) and X2=P(2)(X) (P being a circular permutation map applied on X) in a population of tRNAs. This approach identifies X motifs in the 5' and/or 3' regions of 16 isoaccepting tRNAs (except for the tRNAs Arg, His, Ser and Trp). The statistical analyses are performed on different and large tRNA populations according to the taxonomy (prokaryotes and eukaryotes), tRNA length and tRNA score. Finally, a circular code property observed in genes of prokaryotes and eukaryotes is identified in the 3' regions of 19 isoaccepting tRNAs of prokaryotes and eukaryotes (except for the tRNA Leu). The identification of X motifs and a gene circular code property in tRNAs strengthens the concept proposed in Michel (2012) of a possible translation (framing) code based on a circular code.
authors.affiliation: Equipe de Bioinformatique Théorique, BFO, ICube, Université de Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France. c.michel@unistra.fr
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Michel
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000235:genetics; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics*; D012343:RNA, Transfer / Q000737:chemistry* / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*
chemical_list: D004247:DNA; D012343:RNA, Transfer