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Analysis of Codon Usage Bias in Chloroplast Genomes of Dryas octopetala var. asiatica (Rosaceae). [PDF]

Genes (Basel)
Ling L, Zhang S, Yang T.
europepmc   +1 more source

Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae. [PDF]

BMC Plant Biol
Shen L, Chen S, Liang M, Qu S, Feng S, Wang D, Wang G.   +6 more
europepmc   +1 more source

Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias. [PDF]

Acta Biochim Pol
Mou QH, Hu Z, Zhang J, Daroch M, Tang J.
europepmc   +1 more source

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Codon Usage Bias: An Endless Tale

Journal of Molecular Evolution, 2021
Since the genetic code is degenerate, several codons are translated to the same amino acid. Although these triplets were historically considered to be "synonymous" and therefore expected to be used at rather equal frequencies in all genomes, we now know that this is not the case. Indeed, since several coding sequences were obtained in the late '70s and
Andrés Iriarte, Guillermo Lamolle, Héctor Musto   +2 more
openaire   +2 more sources

Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias

Evolutionary Bioinformatics, 2010
We propose a simple, sensitive measure of synonymous codon usage bias, the Relative Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and unbiased regions, compared with the widely used Codon Adaptation Index (CAI). CAI is a geometric mean of the relative usage of codons in a gene, and is calculated using the codon ...
Soohyun Lee, Changwon Kang
exaly   +5 more sources

Codon Usage Bias and tRNA Abundance in Drosophila

Journal of Molecular Evolution, 1997
Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development. We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the ...
Jeffrey R Powell
exaly   +3 more sources

Codon Usage in Trypanosomatids: The Bias of Expression

Trends in Parasitology, 2018
Translation and RNA decay, two processes in which all mRNAs are engaged, are intimately related processes. Two new studies demonstrate that, in trypanosomatids, codon usage largely shapes mRNA abundance in a translation-dependent manner. The findings indicate that mRNA decay control by codon choice is an ancient and conserved mechanism.
Esteban D, Erben, Christine, Clayton
openaire   +2 more sources

Codon usage bias of Catharanthus roseus

China Journal of Chinese Materia Medica, 2016
This study aimed to provide guidance for the heterogenous gene expression, gene prediction and species evolution by analyzing codon usage bias of Catharanthus roseus.The codon composition and usage bias of 30 437 high-confidence coding sequences from C.roseus were analyzed and the proportion of rare codons of Escherichia coli and Saccharomyces ...
Ying, Li, Xue-Jun, Kuang, Xiao-Xuan, Zhu, Ying-Jie, Zhu, Chao, Sun   +4 more
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Genome-wide analysis of codon usage bias in Ebolavirus

Virus Research, 2015
Ebola virus (EBOV) is a member of the family Filoviridae and its genome consists of a 19-kb, single-stranded, negative sense RNA. EBOV is subdivided into five distinct species with different pathogenicities, being Zaire ebolavirus (ZEBOV) the most lethal species.
Juan Cristina, Pilar Moreno, Héctor Musto   +2 more
exaly   +3 more sources

Codon usage bias in herpesvirus

Archives of Virology, 2010
In this study, I present a comprehensive analysis of codon usage bias in 43 herpesviruses for which the whole genome has been sequenced. The values of the effective number of codons revealed that the majority of the herpesviruses did not have high codon bias, with the exceptions of only simplexviruses and some varicelloviruses.
openaire   +2 more sources