Relative Codon Adaptation

The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new...

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Detalles Bibliográficos
Autores: Fox, Jesse M., Erill, Ivan|||0000-0002-7280-7191
Tipo de recurso: artículo
Fecha de publicación:2010
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:288363
Acceso en línea:https://ddd.uab.cat/record/288363
https://dx.doi.org/urn:doi:10.1093/dnares/dsq012
Access Level:acceso abierto
Palabra clave:Codon bias index
Gene expression
Codon usage
Escherichia coli
Highly expressed genes
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spelling Relative Codon AdaptationA Generic Codon Bias Index for Prediction of Gene ExpressionFox, Jesse M.Erill, Ivan|||0000-0002-7280-7191Codon bias indexGene expressionCodon usageEscherichia coliHighly expressed genesThe development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias. 22010-01-0120102010-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/288363https://dx.doi.org/urn:doi:10.1093/dnares/dsq012reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2883632026-06-06T12:50:31Z
dc.title.none.fl_str_mv Relative Codon Adaptation
A Generic Codon Bias Index for Prediction of Gene Expression
title Relative Codon Adaptation
spellingShingle Relative Codon Adaptation
Fox, Jesse M.
Codon bias index
Gene expression
Codon usage
Escherichia coli
Highly expressed genes
title_short Relative Codon Adaptation
title_full Relative Codon Adaptation
title_fullStr Relative Codon Adaptation
title_full_unstemmed Relative Codon Adaptation
title_sort Relative Codon Adaptation
dc.creator.none.fl_str_mv Fox, Jesse M.
Erill, Ivan|||0000-0002-7280-7191
author Fox, Jesse M.
author_facet Fox, Jesse M.
Erill, Ivan|||0000-0002-7280-7191
author_role author
author2 Erill, Ivan|||0000-0002-7280-7191
author2_role author
dc.subject.none.fl_str_mv Codon bias index
Gene expression
Codon usage
Escherichia coli
Highly expressed genes
topic Codon bias index
Gene expression
Codon usage
Escherichia coli
Highly expressed genes
description The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias.
publishDate 2010
dc.date.none.fl_str_mv 2
2010-01-01
2010
2010-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/288363
https://dx.doi.org/urn:doi:10.1093/dnares/dsq012
url https://ddd.uab.cat/record/288363
https://dx.doi.org/urn:doi:10.1093/dnares/dsq012
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by-nc/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
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