title: Frameshift signals in genes associated with the circular code.
abstract: Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i. e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring methods are developed, a function P based on this code X and a function Q based both on this code X and the 4 trinucleotides with identical nucleotides. They detect a significant correlation between the code X and the -1 frameshift signals in both eukaryotic and prokaryotic genes, and the +1 frameshift signals in eukaryotic genes.
authors: Equipe de Bioinformatique Théorique, LSIIT (UMR CNRS-ULP 7005), Université Louis Pasteur de Strasbourg, Pô1e API, Boulevard Sébastien Brant, 67400 Illkirch, France.
authors: Ahmed
authors: A
authors: Ahmed
authors: Gabriel
authors: G
authors: Frey
authors: Christian J
authors: CJ
authors: Michel
mesh_terms: D000818:Animals; D003062:Codon / Q000235:genetics; D004247:DNA / Q000235:genetics; D005057:Eukaryotic Cells / Q000502:physiology*; D018965:Frameshifting, Ribosomal; D005796:Genes / Q000502:physiology*; D005815:Genetic Code; D006801:Humans; D008957:Models, Genetic; D011387:Prokaryotic Cells / Q000502:physiology*
chemical_list: D003062:Codon; D004247:DNA