Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models

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Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.

Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and the codon usage, use this bias to predict the expression level of genes. When these indices were first introduced, they were based on fairly simple assumptions about which genes are most highly expre...

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Revisiting the CAI from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models

Highly expressed genes in many bacteria and small eukaryotes often have a strong compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI) and the codon usage, use this bias to predict the expression level of genes. Both indices are based on fairly simple assumptions about which genes are most highly expressed, which were known when they we...

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Revisiting the Codon Adaptation Index from a Whole-genome Perspective: Gene Expression, Codon Bias, and Metabolic Networks in the Context of Genomes Comparison

Facts and ideas presented in this short review concern some recent developments at the interface between sequence analysis, gene expression prediction and genome comparison carried on in our group. The guiding line to all results presented here is to derive biological information from genome sequences by means of a purely statistical analysis and an appropriate design of algorithms. 1 Some back...

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ژورنال

عنوان ژورنال: Nucleic Acids Research

سال: 2003

ISSN: 1362-4962

DOI: 10.1093/nar/gkg306