Compare the differences of synonymous codon usage between the two species within cardiovirus [PDF]
, 2011 Background Cardioviruses are positive-strand RNA viruses in the Picornaviridae family that can cause enteric infection in rodents and also been detected at lower frequencies in other mammals such as pigs and human beings.
Wen-qian Liu +7 more
core +2 more sources
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes [PDF]
, 2004 Background Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported.
Xiu-Feng Wan +3 more
core +2 more sources
Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9. [PDF]
Proc Natl Acad Sci U S A, 2016 Newman ZR +3 more
europepmc +2 more sources
Enhanced effective codon numbers to understand codon usage bias [PDF]
Biosystems, 2019 AbstractCodon 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 organisms have ...
openaire +2 more sources
Codon adaptation index as a measure of dominating codon bias [PDF]
Bioinformatics, 2003 Abstract We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a ‘universal’ measure of codon bias.
Carbone, Alessandra +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
doaj +1 more source
Evolution of Codon Usage Bias in Diatoms [PDF]
Genes, 2019 Codon usage bias (CUB)—preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency.
Krasovec, Marc, Filatov, Dmitry
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Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias [PDF]
Molecular Biology and Evolution, 2021 Abstract Alternative synonymous codons are often used at unequal frequencies. Classically, studies of such codon usage bias (CUB) attempted to separate the impact of neutral from selective forces by assuming that deviations from a predicted neutral equilibrium capture selection.
Janaina Lima de Oliveira +5 more
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Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses [PDF]
, 2014 tRNA (tRNA) is a key molecule used for protein synthesis, with multiple points of stress-induced regulation that can include transcription, transcript processing, localization and ribonucleoside base modification.
Begley, Thomas J. +2 more
core +1 more source
Synthetic gene design - The rationale for codon optimization and implications for molecular pharming in plants. [PDF]
, 2017 Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons.
Ma, JK-C, Teh, AY-H, Webster, G
core +1 more source