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Genome Biol. 2005;6(3):R28. Epub 2005 Feb 15.

Comparative context analysis of codon pairs on an ORFeome scale.

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  • 1Centre for Cell Biology, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal. gmoura@bio.ua.pt


Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context.

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