Sentence examples for based on codon adaptation from inspiring English sources

For example, phage BP-4795 (NC_004813), phage cdtI (NC_009514), and 10 other dsDNA phages have negative slopes between PU and φ (Table 3), contrary to what we would have predicted based on codon adaptation.

All three were predicted to be low expressed based on codon usage by the PLS model.

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).

Therefore, our model, rather than rely on CUB, is based on codon frequencies.

These include: 1) decoding time based on the codon adaptation index (D T C A I ), which calculates the codon bias in highly expressed genes (Sharp and Li 1987) and 2) decoding time based on the tRNA adaptation index (D T t A I ) (dos Reis et al. 2004), which takes into consideration the number of tRNA copies in the genome recognizing each codon and additional codon/anticodon interactions.

ORFs were also classified into highly expressed and non-highly expressed genes based on the codon adaptation index (CAI) calculated using CAIJava tool [ 52].

(V2) VIABLE High confidence for viable mutations (novel codon predictions) is assigned based on codons observed in the expanded library (eg, DENV-1234 codon frequency matrix; Observation O4).

Strand asymmetry strongly influences the efficiency of selection on codon adaptation and needs to be taken into account when studying codon adaptation.

The effect of strand asymmetry on codon adaptation observed in dsDNA phages is also visible in ssDNA phages.

However, selection on codon adaptation is present only for mRNAs with efficient initiation; i.e., one should expect little selection for codon adaptation in genes whose mRNAs have poor translation initiation efficiency.