CBDB: The codon bias database [PDF]
BMC Bioinformatics, 2012 Background In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift ...
Hilterbrand Adam +2 more
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Codon Bias Patterns of E. coli's Interacting Proteins. [PDF]
PLoS ONE, 2015 Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial.
Maddalena Dilucca +4 more
doaj +22 more sources
Codon Usage Bias in Phytoplankton [PDF]
Journal of Marine Science and Engineering, 2022 Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is known about it in phytoplankton.
Marc Krasovec, Dmitry A. Filatov
doaj +4 more sources
Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes [PDF]
Frontiers in Microbiology, 2023 IntroductionCodon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown.MethodsIn this study, we investigated the ...
Peng Wu +8 more
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Relationship between amino acid composition and gene expression in the mouse genome [PDF]
BMC Research Notes, 2011 Background Codon bias is a phenomenon that refers to the differences in the frequencies of synonymous codons among different genes. In many organisms, natural selection is considered to be a cause of codon bias because codon usage in highly expressed ...
Misawa Kazuharu, Kikuno Reiko F
doaj +3 more sources
Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues [PDF]
BMC Genomics, 2021 Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution.
Giovanni Franzo +3 more
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Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias [PDF]
Cell Reports, 2016 Codon pair bias is a remarkably stable characteristic of a species. Although functionally uncharacterized, robust virus attenuation was achieved by recoding of viral proteins using underrepresented codon pairs.
Dusan Kunec, Nikolaus Osterrieder
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A model for codon position bias in RNA editing [PDF]
Physical Review Letters, 2005 RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias
Bundschuh, Ralf, Liu, Tsunglin
core +6 more sources
Mapping evolutionary paradigm of Oropouche virus driven by dinucleotide bias and context-dependent codon bias [PDF]
VirulenceArthropod-borne viruses (arboviruses) pose significant public health threats, and understanding their evolutionary mechanisms can inform molecular diagnostics and vaccine design.
Xuanye Yang +4 more
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Codon bias among synonymous rare variants is associated with Alzheimer's disease imaging biomarker. [PDF]
Pac Symp Biocomput, 2018 Alzheimer's disease (AD) is a neurodegenerative disorder with few biomarkers even though it impacts a relatively large portion of the population and is predicted to affect significantly more individuals in the future.
Miller JE +6 more
europepmc +3 more sources