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Analysis of selection in protein-coding sequences accounting for common biases.
Del Amparo, Roberto; Branco, Catarina; Arenas, Jesús; Vicens, Alberto; Arenas, Miguel.
Afiliação
  • Del Amparo R; CINBIO (Biomedical Research Center), University of Vigo, 36310 Vigo, Spain.
  • Branco C; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
  • Arenas J; CINBIO (Biomedical Research Center), University of Vigo, 36310 Vigo, Spain.
  • Vicens A; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain.
  • Arenas M; Unit of Microbiology and Immunology, University of Zaragoza, 50013 Zaragoza, Spain.
Brief Bioinform ; 22(5)2021 09 02.
Article em En | MEDLINE | ID: mdl-33479739
The evolution of protein-coding genes is usually driven by selective processes, which favor some evolutionary trajectories over others, optimizing the subsequent protein stability and activity. The analysis of selection in this type of genetic data is broadly performed with the metric nonsynonymous/synonymous substitution rate ratio (dN/dS). However, most of the well-established methodologies to estimate this metric make crucial assumptions, such as lack of recombination or invariable codon frequencies along genes, which can bias the estimation. Here, we review the most relevant biases in the dN/dS estimation and provide a detailed guide to estimate this metric using state-of-the-art procedures that account for such biases, along with illustrative practical examples and recommendations. We also discuss the traditional interpretation of the estimated dN/dS emphasizing the importance of considering complementary biological information such as the role of the observed substitutions on the stability and function of proteins. This review is oriented to help evolutionary biologists that aim to accurately estimate selection in protein-coding sequences.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Seleção Genética / Proteínas / Fases de Leitura Aberta / Evolução Molecular / Mutação de Sentido Incorreto / Modelos Genéticos Tipo de estudo: Guideline Idioma: En Ano de publicação: 2021 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Seleção Genética / Proteínas / Fases de Leitura Aberta / Evolução Molecular / Mutação de Sentido Incorreto / Modelos Genéticos Tipo de estudo: Guideline Idioma: En Ano de publicação: 2021 Tipo de documento: Article