Open Access Method

Comparative context analysis of codon pairs on an ORFeome scale

Gabriela Moura1, Miguel Pinheiro2, Raquel Silva1, Isabel Miranda1, Vera Afreixo2, Gaspar Dias2, Adelaide Freitas3, José L Oliveira2 and Manuel AS Santos1*

Author Affiliations

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

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Genome Biology 2005, 6:R28  doi:10.1186/gb-2005-6-3-r28

Published: 15 February 2005

Abstract

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.