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Molecular Biology and Evolution 18:1838-1840 (2001)
© 2001 Society for Molecular Biology and Evolution

Intragenomic Base Content Variation Is a Potential Source of Biases When Searching for Horizontally Transferred Genes

Stéphane Guindon and Guy Perrière

Laboratoire d'Informatique de Robotique et de Microelectronique de Montpellier, Montpellier, France;
Laboratoire de Biométrie et Biologie Évolutive–UMR Centre National de la Recherche Scientifique 5558, Université Claude Bernard–Lyon 1, Villeurbanne, France

Horizontal transfers in bacteria have been extensively studied, and most of the methods developed to identify transferred sequences are based on the assumption that exogenous genes have characteristics that differ from those shared by endogenous ones. Up to now, the most common way to look at the peculiar characteristics exhibited by "alien" sequences has been to analyze biases in synonymous codon usage (Médigue et al. 1991Citation ; Lawrence and Ochman 1997, 1998Citation ; Aravind et al. 1998Citation ; Karlin, Campbell, and Mrazek 1998Citation ; Karlin, Mrazek, and Campbell 1998Citation ; Nelson et al. 1999Citation ). The main underlying hypothesis of this approach is that synonymous codons presented by genes coming from distantly related species are different from those shared by endogenous sequences. In this paper, we show that the results obtained may be biased due to intragenomic base content variations that may occur in bacterial genomes.

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