Comparative context analysis of codon pairs on an ORFeome scale.
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.
Moura
Gabriela
G
Centre for Cell Biology, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal. gmoura@bio.ua.pt
Pinheiro
Miguel
M
Silva
Raquel
R
Miranda
Isabel
I
Afreixo
Vera
V
Dias
Gaspar
G
Freitas
Adelaide
A
Oliveira
José L
JL
Santos
Manuel A S
MA
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
D003062:Codon; D012333:RNA, Messenger