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 ORFeom...

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Detalles Bibliográficos
Autores principales: Moura, Gabriela, Pinheiro, Miguel, Silva, Raquel, Miranda, Isabel, Afreixo, Vera, Dias, Gaspar, Freitas, Adelaide, Oliveira, José L, Santos, Manuel AS
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088947/
https://www.ncbi.nlm.nih.gov/pubmed/15774029
http://dx.doi.org/10.1186/gb-2005-6-3-r28
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author Moura, Gabriela
Pinheiro, Miguel
Silva, Raquel
Miranda, Isabel
Afreixo, Vera
Dias, Gaspar
Freitas, Adelaide
Oliveira, José L
Santos, Manuel AS
author_facet Moura, Gabriela
Pinheiro, Miguel
Silva, Raquel
Miranda, Isabel
Afreixo, Vera
Dias, Gaspar
Freitas, Adelaide
Oliveira, José L
Santos, Manuel AS
author_sort Moura, Gabriela
collection PubMed
description 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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spelling pubmed-10889472005-05-05 Comparative context analysis of codon pairs on an ORFeome scale Moura, Gabriela Pinheiro, Miguel Silva, Raquel Miranda, Isabel Afreixo, Vera Dias, Gaspar Freitas, Adelaide Oliveira, José L Santos, Manuel AS Genome Biol Method 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. BioMed Central 2005 2005-02-15 /pmc/articles/PMC1088947/ /pubmed/15774029 http://dx.doi.org/10.1186/gb-2005-6-3-r28 Text en Copyright © 2005 Moura et al.; licensee BioMed Central Ltd.
spellingShingle Method
Moura, Gabriela
Pinheiro, Miguel
Silva, Raquel
Miranda, Isabel
Afreixo, Vera
Dias, Gaspar
Freitas, Adelaide
Oliveira, José L
Santos, Manuel AS
Comparative context analysis of codon pairs on an ORFeome scale
title Comparative context analysis of codon pairs on an ORFeome scale
title_full Comparative context analysis of codon pairs on an ORFeome scale
title_fullStr Comparative context analysis of codon pairs on an ORFeome scale
title_full_unstemmed Comparative context analysis of codon pairs on an ORFeome scale
title_short Comparative context analysis of codon pairs on an ORFeome scale
title_sort comparative context analysis of codon pairs on an orfeome scale
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088947/
https://www.ncbi.nlm.nih.gov/pubmed/15774029
http://dx.doi.org/10.1186/gb-2005-6-3-r28
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