Comparative context analysis of codon pairs on an ORFeome scale
1 Centre for Cell Biology, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
2 Institute of Electronics and Telematics Engineering, University of Aveiro, 3810-193 Aveiro, Portugal
3 Department of Mathematics, University of Aveiro, 3810-193 Aveiro, Portugal
Genome Biology 2005, 6:R28 doi:10.1186/gb-2005-6-3-r28Published: 15 February 2005
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.