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We compared levels of nucleotide diversity in miRNA to other genomic sequence classes (for examples, exons and introns) in each population group using Watterson's estimator of theta (θW).
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Thus, from the three species alignments, we calculated the GC content for each functional sequence class for each aligned fragment.
For each sequence class, for each integer period, we evaluated the fraction of sequences that returned a nominally significant BWB test probability (P BWB period-10) < 0.05).
Repeats are the least alignable sequence class for the Hs-Gg genome pair, whereas the proportion of repeats and non-coding sequence aligned for Dm-Dv is extremely similar.
On the other hand, the complete sequences of the microarray printed clones – although may be the ultimate sequence class for comparisons – are not available for the tomato and potato arrays.
The mean Tajima's D values were positive and very close to zero for all of the sequence classes except for synonymous sites for which the distribution was more positively skewed compared with the other classes (table 2).
Let us next look at the other sequence classes appearing for lower μ values.
We saw that four sequence classes can coexist for μ = 0.004.
Two sequences, G12SD-1 and G12SD-2, from the two dominating sequence classes were arbitrarily chosen for further examination.
Second, the X and the autosomes show comparable α* estimates among all sequence classes except synonymous substitutions, for which α* is significantly higher on the X (0.372 vs. 0.277).
Genomic divergences and substitution rates were examined for each clone and for various sequence classes under different functional constraints.
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CEO of Professional Science Editing for Scientists @ prosciediting.com