If the variant falls within an exon, new codons for each variant allele are derived and compared to the reference codon.
First, we determine whether our RK-gag has increased expression as compared to the codon optimized version, AD-gag.
Furthermore, GAG is not underrepresented at the 5' exon boundary compared to the synonymous GAA codon [ 31].
These predictions were compared to the start codons predicted through the proteogenomic mapping process using Perl.
This genome composition bias leads to the usage of some codons at a higher frequency as compared to the synonymous codons for encoding the particular amino acid.
By contrast, during biofilm entry, median ribosome density was significantly higher at serine and cysteine codons as compared to the remaining codons, suggesting that the translation speed of ribosomes is selectively reduced at these codons during biofilm entry.
The gene copy number of each tRNA isoacceptor was calculated and compared to the total number of cognate codons present in coding sequences for each species.
Our model predicts a difference in these rates simply because of the higher frequency of frame-shift stop codons compared to the frequency of frame-shift start codons.
A possible explanation for the improved expression charateristics of "dkr" compared to the complete ORF may be indicated by codon usage analysis: Compared to L. lactis subsp. cremoris MG1363 and Lb.
As a result, when compared to the normal open reading frame, an additional codon is inserted.
