Results 41 to 50 of about 52,855 (250)
Site-Specific Codon Bias in Bacteria [PDF]
Genetics, 1996 Abstract Sequences of the gapA and ompA genes from 10 genera of enterobacteria have been analyzed. There is strong bias in codon usage, but different synonymous codons are preferred at different sites in the same gene. Site-specific preference for unfavored codons is not confined to the first 100 codons and is usually manifest between ...
J M, Smith, N H, Smith
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Codon bias and plasticity in immunoglobulins [PDF]
Molecular Biology and Evolution, 1997 Immunoglobulin genes experience Darwinian evolution twice. In addition to the germline evolution all genes experience, immunoglobulins are subjected, upon exposure to antigen, to somatic hypermutation. This is accompanied by selection for high affinity to the eliciting antigen and frequently results in a significant increase in the specificity of the ...
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Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle [PDF]
Molecular Biology and Evolution, 2004 New and simple numerical criteria based on a codon adaptation index are applied to the complete genomic sequences of 80 Eubacteria and 16 Archaea, to infer weak and strong genome tendencies toward content bias, translational bias, and strand bias. These criteria can be applied to all microbial genomes, even those for which little biological information
Carbone, Alessandra +2 more
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Forces that influence the evolution of codon bias [PDF]
Philosophical Transactions of the Royal Society B: Biological Sciences, 2010 The frequencies of alternative synonymous codons vary both among species and among genes from the same genome. These patterns have been inferred to reflect the action of natural selection. Here we evaluate this in bacteria. While intragenomic variation in many species is consistent with selection favouring translationally optimal codons, much of the ...
Sharp, Paul M. +2 more
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Analysis of synonymous codon usage in Hepatitis A virus
Virology Journal, 2011 Background Hepatitis A virus is the causative agent of type A viral hepatitis, which causes occasional acute hepatitis. Nevertheless, little information about synonymous codon usage pattern of HAV genome in the process of its evolution is available.
Ma Lina +8 more
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Mitochondrial DNA. Part B. Resources, 2020 Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly ...
Zhiwen Chen +10 more
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Enhanced effective codon numbers to understand codon usage bias [PDF]
Biosystems, 2019 Abstract Codon usage bias is a well recognized phenomenon but the relative influence of its major causes: G+C content, mutational biases, and selection, are often difficult to disentangle. This paper presents methods to calculate modified effective codon numbers that allow the investigation of the sources of codon bias and how genes or ...
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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 in choosing the positions of the editing sites.
Liu, Tsunglin, Bundschuh, Ralf
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Differences in codon bias cannot explain differences in translational power among microbes
BMC Bioinformatics, 2005 Background Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes,
Dethlefsen Les, Schmidt Thomas M
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Mechanism of Virus Attenuation by Codon Pair Deoptimization
Cell Reports, 2020 Summary: Codon pair deoptimization is an efficient virus attenuation strategy, but the mechanism that leads to attenuation is unknown. The strategy involves synthetic recoding of viral genomes that alters the positions of synonymous codons, thereby ...
Nicole Groenke +10 more
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