title: Comparative context analysis of codon pairs on an ORFeome scale.
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.
authors.affiliation: Centre for Cell Biology, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal. gmoura@bio.ua.pt
authors.forename: Gabriela
authors.initials: G
authors.lastname: Moura
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinheiro
authors.forename: Raquel
authors.initials: R
authors.lastname: Silva
authors.forename: Isabel
authors.initials: I
authors.lastname: Miranda
authors.forename: Vera
authors.initials: V
authors.lastname: Afreixo
authors.forename: Gaspar
authors.initials: G
authors.lastname: Dias
authors.forename: Adelaide
authors.initials: A
authors.lastname: Freitas
authors.forename: José L
authors.initials: JL
authors.lastname: Oliveira
authors.forename: Manuel A S
authors.initials: MA
authors.lastname: Santos
mesh_terms: D002176:Candida albicans / Q000235:genetics; D016000:Cluster Analysis; D003062:Codon; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D016366:Open Reading Frames / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics; D012984:Software
chemical_list: D003062:Codon; D012333:RNA, Messenger