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Genetica. 2018 Feb;146(1):53-63. doi: 10.1007/s10709-017-9996-4. Epub 2017 Oct 14.

Codon usage and amino acid usage influence genes expression level.

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Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.


Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.


Amino acid; Codon; Gene expression; Medicago truncatula

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