Sentence examples similar to and calculating it based on the codon from inspiring English sources

In B. subtilis the proportion of the tRNAs pairing to more than one codon is calculated based on the codon usage ratio.

The translation efficiency was calculated based on the codon usage, giving maximum 4-fold decrease in Triticum aestivum.

The GC-contents were calculated based on the codon usage statistics tool CHIPS via the Mobyle-webpage http://mobyle.pasteur.fr.pasteur.fr

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).

The probabilities of codon bias for the six conserved cysteines and for the arginine residue responsible of the posttranslational pro region cleavage were calculated assuming a binomial distribution, based on the codon usage inferred from the M. galloprovincialis transcriptome (Gerdol et al. 2014) and using the tool "cusp" included in the EMBOSS package (Rice et al. 2000).

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

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.

Codon optimization was performed based on the codon table of Kazusa DNA Research Institute (Kisarazu, Japan).

Ks was estimated based on the codon alignments.

Figure 1 Nucleotide sequences of TcTrx cDNA and its codon usage optimization based on the yeast codon usage table.

The relative codon bias between sets of genes in the two focal species, P. falciparum and T. annulata, was calculated based on the method developed by Karlin et al. [ 44].