Sentence examples for using the base substitution from inspiring English sources
We estimated the mutation rate using the base substitution data generated by the Bowtie and VarScan pipeline.
Since both methods include consideration of mutations in specific genes, we believe that part of the increased performance of our method stems from using the base substitution frequencies, which reflect the mutational processes that shaped the genome of the tumor [ 13].
This corrected divergence was then translated to estimate the insertion date of the elements at their present location, using the average base substitution rate derived from the grass adh1-adh2 region of 6.5 × 10-9 substitution per site per year [ 41], given the assumption of a uniform mutation rate in grapevine.
The Ti/Tv and nonsynonymous/synonymous ratios were calculated in R using the exonic base substitutions.
Using the novel consensus sequence, the base substitution rate for each position in the genome was again calculated (Figure 3B).
RSEARCH used the base pair and single nucleotide substitution matrix RIBOSUM to find optimal structural alignments between a RNA sequence and a sequence database.
Observed pairwise sequence divergences were corrected using a base substitution model which best fitted the DNA data by applying a likelihood ratio test (implemented in Modeltest V 3.0; [ 42]).
The insertion dates were estimated using an average base substitution rate of 1.3 E-8 (Ma and Bennetzen 2004).
For each tumor sample, we used all base substitution mutations, regardless of their effect, to calculate the relative frequencies of the six different classes of single base substitutions.
Estimation of Ka/Ks (dN/dS) ratios was then carried out by maximum likelihood using the pairwise codon-based substitution model in Codeml, which is part of the Phylogenetic Analysis by Maximum Likelihood (PAML) suite of programs [ 100].
To produce mutated plasmids, site-directed mutation was used to introduce base substitution to the miR-133 binding site of luciferase reporters using Site-Directed Gene Mutagenesis Kit (Beyotime).
