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Circular Code Signal in Frameshift Genes | OMICS International | Abstract
ISSN: 0974-7230

Journal of Computer Science & Systems Biology
Open Access

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Research Article

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]
[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.

Abstract

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.

Keywords

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