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DNA Research Advance Access published online on September 16, 2008
DNA Research, doi:10.1093/dnares/dsn021
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© The Author 2008. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Detecting Horizontally Transferred and Essential Genes Based on Dinucleotide Relative Abundance

Robert H. Baran and Hanseok Ko*

Department of Electronics and Computer Engineering, Korea University, Anam-dong, Sungbuk-ku, Seoul 136-702, South Korea

Received 12 December 2007 ; accepted 5 August 2008.

Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes.

Key words: amelioration; dinucleotide frequency; essential genes; horizontal transfer; molecular evolution

* To whom correspondence should be addressed. Tel. +82 2-3290-3239. Fax. +82 2-3291-2450. E-mail: hsko{at}korea.ac.kr

Edited by Katsumi Isnono


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