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The presence of saturation in base substitution for each of the alignments was tested using DAMBE5 [ 20].
For the Bayesian analysis, we used the program MrModeltest 2.2 [ 42] to select an appropriate model of base substitution for each gene partition.
At the nucleotide sequence level, the gene segments between the two assemblies are surprisingly diverged to a degree that is significantly higher than the genomic average rate of one base substitution for each 1,200 bp, or 0.08%.
The presence of saturation in base substitution for each of the gene alignment was tested by comparing half of the theoretical saturation index expected when assuming full saturation (Iss.c, critical value) with the observed saturation index (Iss).
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To see how vector proteins respond to point mutations, we used Stylus to generate and score 100,000 random single base substitutions for each of the 10 homologous genes produced in the preceding example.
There was a perfect match to P1-wr [W23] sequence at the 5' end and near perfect match at the 3' end (We detected a possible base substitution for the P1-mm-542A P1-mm-542A P1-mm-542A.
These motifs will typically require only a single base substitution for transformation into the other motif.
The latter approach allowing only the detection of an IDH2 mutation presence, we have only the type of base substitution for 15 tumors.
Using the novel consensus sequence, the base substitution rate for each position in the genome was again calculated (Figure 3B).
To calculate base substitution rates for each CGI, alignments of orthologous regions between human, chimpanzee, and their ancestral sequences were used.
Somatic mosaicism is thought to result from de novo gain-of-function-type mutations that are introduced at a very early and limited stage of development, and it is reasonable to focus our efforts on detecting base substitutions for somatic mosaicism in the NLRP3 gene.
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