Circular Code Signal in Frameshift Genes
Ahmed Ahmed and Christian J. Michel*
Equipe de Bioinformatique Théorique, FDBT, LSIIT (UMR UdS-CNRS 7005), Université de Strasbourg, Pôle API, Boulevard Sébastien Brant, 67400 ILLKIRCH, FRANCE
- *Corresponding Author:
- Dr. Christian J. Michel
Equipe de Bioinformatique
Théorique, FDBT, LSIIT (UMR UdS-CNRS 7005)
Université de Strasbourg, Pôle
API, Boulevard Sébastien Brant
67400 ILLKIRCH, France
E-mail: [email protected]
Received date: January 07, 2011; Accepted date: January 18, 2011; Published date: January 20, 2011
Citation: Ahmed A, Michel CJ (2011) Circular Code Signal in Frameshift Genes. J Comput Sci Syst Biol 4:007-015. doi:10.4172/jcsb.1000069
Copyright: © 2011 Ahmed A, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
A trinucleotide circular code is a set of trinucleotides allowing the reading frame in genes to be retrieved locally, i.e. anywhere in genes and in particular without start codon, and automatically with a window of a few nucleotides. In 1996, a common circular code X has been identified simultaneously in two large populations of eukaryotic and prokaryotic genes. The method proposed here identifies periodic signals of this code X in the two frameshift types (+1 and -1) of both eukaryotic and prokaryotic frameshift genes. As expected by the code theory, the circular code modulo 3 signals move in the same direction of translational frameshifting. Finally, in 68% of frameshift genes in the RECODE 2 database, the frameshift type (+1 and -1) is automatically identified using only this circular code periodic signal. This circular code information constitutes a new structural property of frameshift genes. It may be used directly or in association with existing methods to identify frameshift genes in genomes and their encoded proteins.