Analysis of codon usage patterns of bacterial genomes using the self-organizing map

Molecular Biology and Evolution
H C WangM Li

Abstract

Codon usage varies both between organisms and between different genes in the same organism. This observation has been used as a basis for earlier work in identifying highly expressed and horizontally transferred genes in Escherichia coli. In this work, we applied Kohonen's self-organizing map to analysis of the codon usage pattern of the Escherichia coli, Aquifex aeolicus, Archaeoglobus fulgidus, Haemophilus influenzae RD:, Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Pyrococcus horikoshii genomes for evidence of highly expressed genes and horizontally transferred genes. All of the analyzed genomes had a clear category of horizontally transferred genes, and their apparent percentages ranged from 7.7% to 21.4%. The apparent percentage of highly expressed genes ranges from 0% to 11.8%. A clustering of average codon usage of main gene categories of the seven genomes showed an interesting mixing of gene classes in four thermophilic/hyperthermophilic organisms, A. aeolicus, A. fulgidus, M. thermoautotrophicum, and P. horikoshii, which suggests possible origins of their horizontally transferred genes as well as the need for adaptation to a specific environment. Further classification of the three gene categorie...Continue Reading

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Citations

Oct 30, 2001·Current Opinion in Genetics & Development·M A Ragan
Jan 14, 2005·Bioinformatics·Shaun MahonyDaniel S Rokhsar
Feb 3, 2007·Bioinformatics·Robert G Beiko, Robert L Charlebois
Oct 5, 2002·Nucleic Acids Research·David J LynnDonal A Hickey
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Jul 1, 2006·Algorithms for Molecular Biology : AMB·Peter MeinickeStephan Waack
May 10, 2006·PLoS Computational Biology·Marc Bailly-BechetMassimo Vergassola
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Aug 9, 2002·Theoretical Population Biology·Ravi JainJames A Lake

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