Sentence examples for based on codon frequency from inspiring English sources
No predictive model based on codon frequency could be obtained after randomization for either the polymerase dataset (Best model: R2 = 0.037, Cross-Val R2 = 0.004), the reduced scFv dataset (Best model: R2 = 0.44, Cross-Val R2 = 0.30) or the combined dataset (Best Cross-Val R2 = 0.11).
This can be achieved by a more detailed compositional argument, one that is based on codon frequencies.
Because CAI is based on codon frequencies of a gene with respect to the codon usage of a reference set of genes known to be highly expressed, short sequences with few codons may produce unreliable CAI values.
The use of other coding scores, for example based on codon frequencies instead of hexamer frequencies or related metrics such as GC content produced consistent results.
Another common technique for genome classification is based on codon usage frequencies [ 43].
However, another study suggested that three-base periodicity in biological sequences had specific characteristics not reproduced in computer-generated exon-like sequences based on codon usage frequencies [ 14].
Log likelihood ratios (LLRs) for each codon were calculated based on the codon frequency conditional of the encoded amino acid, such that for each codon i coding for amino acid a i, LLR i = log2 c i /n i ), in which c i and n i correspond to the likelihood of codon i conditional on amino acid a i in coding and non-coding sequences respectively (Additional file 4).
COrrespondence Analysis of codon usage (COA) was calculated based on codon usage as well as Relative Synonymous Codon Usage (RSCU).
The codons for sTfR were optimized using human preferred codons based on Codon Usage Database (Kazusa DNA Research Institute, Japan).
We plotted percentage errors of Ks against κR (assuming κY = 3.75; Figure 2A to 2C) based on human codon frequencies, showing similar results when taking equal or rice codon frequencies (data not shown).
