Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS‐CoV‐2 mitigation strategies
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Medical Virology"
DOI: 10.1002/jmv.27056
Abstract: Since the start of the coronavirus disease 2019 (COVID‐19) pandemic, the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has rapidly widespread worldwide becoming one of the major global public health issues of the last centuries.… read more here.
Keywords: analysis reveals; betacoronaviruses genome; analysis; codon usage ... See more keywords
The nucleotide usages significantly impact synonymous codon usage in Mycoplasma hyorhinis
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Basic Microbiology"
DOI: 10.1002/jobm.202000592
Abstract: Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics… read more here.
Keywords: synonymous codon; hyorhinis; codon usage; mycoplasma hyorhinis ... See more keywords
Tailoring Codon Usage to the Underlying Biology for Protein Expression Optimization.
Sign Up to like & getrecommendations! Published in 2022 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1859-2_4
Abstract: For heterologous gene expression, codon optimization is required to enhance the quality and quantity of the protein product. Recently, we introduced the software tool OCTOPOS. This sequence optimizer combines a detailed mechanistic mathematical modeling of… read more here.
Keywords: expression; tailoring codon; optimization; codon usage ... See more keywords
Analysis of codon usage bias of chloroplast genes in Oryza species : Codon usage of chloroplast genes in Oryza species.
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DOI: 10.1007/s00425-020-03470-7
Abstract: MAIN CONCLUSION The codon usage bias in chloroplast genes of Oryza species was low and AT rich. The pattern of codon usage was different among Oryza species and mainly influenced by mutation pressure and natural… read more here.
Keywords: chloroplast genes; oryza species; codon usage; usage bias ... See more keywords
Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage
Sign Up to like & getrecommendations! Published in 2018 at "Archives of Virology"
DOI: 10.1007/s00705-018-3930-7
Abstract: RNA viruses are classified by their genome polarity and replication strategies. Nucleotide composition and codon usage differ among virus groups, for instance positive-sense RNA (+ssRNA) viruses have higher GC-content than the other RNA virus groups.… read more here.
Keywords: genome polarity; rna viruses; ssrna viruses; rna ... See more keywords
Codon usage trend in genes associated with obesity
Sign Up to like & getrecommendations! Published in 2020 at "Biotechnology Letters"
DOI: 10.1007/s10529-020-02931-z
Abstract: Obesity is not only a social menace but also an economic burden as it reduces productivity and increases health care cost. We used bioinformatic tools to analyze the CUB of obesity associated genes and compared… read more here.
Keywords: codon usage; housekeeping genes; obesity; genes associated ... See more keywords
New insights into the codon usage patterns of the bactericidal/permeability-increasing (BPI) gene across nine species.
Sign Up to like & getrecommendations! Published in 2017 at "Gene"
DOI: 10.1016/j.gene.2017.03.016
Abstract: Bactericidal/permeability-increasing (BPI) protein is a member of a new generation of proteins known as super-antibiotics that are implicated as endotoxin neutralising agents. Non-uniform usage of synonymous codons for a specific amino acid during translation of… read more here.
Keywords: codon usage; permeability increasing; bpi gene; bactericidal permeability ... See more keywords
Codon usage pattern and predicted gene expression in Arabidopsis thaliana.
Sign Up to like & getrecommendations! Published in 2019 at "Gene"
DOI: 10.1016/j.gene.2019.100012
Abstract: The extensive research for predicting highly expressed genes in plant genome sequences has been going on for decades. The codon usage pattern of genes in Arabidopsis thaliana genome is a classical topic for plant biologists… read more here.
Keywords: arabidopsis thaliana; pattern; codon usage; gene expression ... See more keywords
Factors influencing codon usage of mitochondrial ND1 gene in pisces, aves and mammals.
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DOI: 10.1016/j.mito.2017.06.004
Abstract: Animal mitochondrial genome harbours 13 protein coding genes which regulate the process of respiration. The mitochondrial NADH dehydrogenase 1 (MT-ND1) gene, one of the 13 protein-coding genes, encodes the NADH dehydrogenase 1 enzyme of the… read more here.
Keywords: analysis; codon usage; nd1 gene; gene ... See more keywords
Analysis of codon usage bias in mitochondrial CO gene among Platyhelminthes.
Sign Up to like & getrecommendations! Published in 2021 at "Molecular and biochemical parasitology"
DOI: 10.1016/j.molbiopara.2021.111410
Abstract: The phenomenon of non-uniform usage of the synonymous codons, where some codons are given more preference to others, is known as codon usage bias (CUB). CUB is known to be determined by two major evolutionary… read more here.
Keywords: codon usage; selection; usage bias; usage ... See more keywords
Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic
Sign Up to like & getrecommendations! Published in 2022 at "Virology"
DOI: 10.1016/j.virol.2022.01.011
Abstract: SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we… read more here.
Keywords: analysis; sars cov; codon usage; synonymous codon ... See more keywords