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

¹Centre for Cell Biology, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal

²Institute of Electronics and Telematics Engineering, University of Aveiro, 3810-193 Aveiro, Portugal

³Department of Mathematics, University of Aveiro, 3810-193 Aveiro, Portugal

author email corresponding author email

Genome Biology 2005, 6:R28doi:10.1186/gb-2005-6-3-r28


Published:	15 February 2005

Subject areas: Bioinformatics, Genome studies, Methods, Evolution

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.