We divided unambiguously aligned sequences into five partitions (first, second, third codon positions, rRNA and tRNA genes) assuming that functional constraints on sequence evolution are more similar within codon positions (or types of molecules) across genes than across codon positions (or types of molecules) within genes.
We set five partitions for the unambiguously aligned nucleotide sequences of the 123nRTn and 12n3rRTn datasets, assuming that functional constraints on sequence evolution are more similar within codon positions (or types of molecule) across genes than across codon positions (or types of molecule) within genes, at least for a set of mitochondrial genes.
We set five (123nRTn and 12n3rRTn) partitions, assuming that functional constraints on sequence evolution are more similar within codon positions (or types of molecules) across genes than across codon positions (or types of molecules) within genes, at least for a set of mitochondrial genes.
In the case of the gene length, genes of 500 or more bp showed a similar codon context bias.
We expected that the genes in a given EB2 dataset and cognate EB1 dataset would be more similar in relation to codon usage than the same set of EB2 genes and a randomly selected set of EB1 genes.
This means that more similar proteins in terms of codon frequency, show similar responses in protein concentration to changes in mRNA, therefore most of the variability in the mRNA-protein relation can be explained by the codon frequency.
Surprisingly, the codon usage bias in the P. caudatum mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related T. pyriformis and other single-celled eukaryotes such as Chlamydomonas, than to the closely related P. tetraurelia.
Single-host Flaviviridae members which persistently infect mammals or insect hosts (Hepacivirus and insect-only Flavivirus, respectively) were found to posses a codon usage profile more similar to that of their hosts than to related Flaviviridae.
In this study we utilized the observation that horizontally transferred genes often exhibit codon usage patterns more similar to that of the donor than that of the acceptor genome.
The stop codon usage is now more similar for across the sets.
