Comparative context analysis of codon pairs on an ORFeome scale.

Gabriela Moura; Miguel Pinheiro; Raquel Silva; Isabel Miranda; Vera Afreixo; Gaspar Dias; Adelaide Freitas; José L. Oliveira; Manuel A. S. Santos

doi:10.1186/gb-2005-6-3-r28

Comparative context analysis of codon pairs on an ORFeome scale.

Gabriela Moura^*, Miguel Pinheiro, Raquel Silva, Isabel Miranda, Vera Afreixo, Gaspar Dias, Adelaide Freitas, José L. Oliveira, Manuel A. S. Santos

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

80 Citations (Scopus)

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.

Original language	English
Pages (from-to)	R28
Journal	Genome Biology
Volume	6
Issue number	3
DOIs	https://doi.org/10.1186/gb-2005-6-3-r28
Publication status	Published - 2005
Externally published	Yes

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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.",

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AU - Moura, Gabriela

AU - Pinheiro, Miguel

AU - Silva, Raquel

AU - Miranda, Isabel

AU - Afreixo, Vera

AU - Dias, Gaspar

AU - Freitas, Adelaide

AU - Oliveira, José L.

AU - Santos, Manuel A. S.

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PY - 2005

Y1 - 2005

N2 - 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.

AB - 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.

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SN - 1474-7596

VL - 6

SP - R28

JO - Genome Biology

JF - Genome Biology

IS - 3

ER -

Comparative context analysis of codon pairs on an ORFeome scale.

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