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The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The codons specify which amino acid will be added next during protein biosynthesis. With some exceptions, [1] a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid.
The Codon Adaptation Index (CAI) is the most widespread technique for analyzing codon usage bias.As opposed to other measures of codon usage bias, such as the 'effective number of codons' (Nc), which measure deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes.
Start codon (blue circle) of the human mitochondrial DNA MT-ATP6 gene. For each nucleotide triplet (square brackets), the corresponding amino acid is given (one-letter code), either in the +1 for MT-ATP8 (in red) or in the +3 frame for MT-ATP6 (in blue). In this genomic region, the two genes . The start codon is the first codon of a messenger ...
Effective number of codons (abbreviated as ENC or Nc) is a measure to study the state of codon usage biases in genes and genomes. [1] The way that ENC is computed has obvious similarities to the computation of effective population size in population genetics. [2] Although it is easy to compute ENC values, it has been shown that this measure is ...
Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation ( stop codons ). There are 64 different codons (61 codons encoding for amino acids ...
In contrast, in a study of codon usage in Phytoplasmas, it was found that 30 out of 78 open reading frames analysed translated better with this code (UGA for tryptophan) than with the bacterial, archaeal and plant plastid code while the remainder showed no differences between the two codes (Melamed et al. 2003).
AGA and AGG were thought to have become mitochondrial stop codons early in vertebrate evolution. [1] However, at least in humans it has now been shown that AGA and AGG sequences are not recognized as termination codons. A -1 mitoribosome frameshift occurs at the AGA and AGG codons predicted to terminate the CO1 and ND6 open reading frames (ORFs ...
Codon usage bias, a measure related to codon frequencies, was one of the first detection methods used in methodical assessments of HGT. This approach requires a host genome which contains a bias towards certain synonymous codons (different codons which code for the same amino acid) which is clearly distinct from the bias found within the donor ...