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In addition, the times to the most recent common ancestor (TMRCA) of the seven geographical groups and the whole population were estimated using the same mutation rate as above.
By comparison, the estimated time for genetic differentiation of the Atlantic and Pacific populations of swordfish and of the Atlantic and Pacific bluefin tunas, using the same mutation rate, is very similar (450 470 Ky), and an even shorter time (170 Ky) is sufficient to explain the substantial genetic differentiation between the Atlantic and Mediterranean swordfish populations [ 30].
> -wrap-foot> As our prediction threshold was derived using the same mutation datasets used in this benchmark (albeit using a leave-one-out analysis), and a large proportion of driver mutations is also present in our training data, we recognize the potential for bias in the observed performances.
Two rates of mutation G- > A and A- > G are an explicit part of the model of stop codon evolution and exactly the same mutations are found in G < − > A two-fold synonymous sites, making it possible to model G-content while using the same mutation rates.
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To investigate the nature of these interactions we performed a series of EMSA experiments using the same mutations as in the transfection experiments and wt (wild type) sequences (Fig. 5D F).
To provide unscaled parameters we used the same mutation rate estimate as described for MIGRATE (see above).
Using the same mutational strategy, mutations were introduced into the ERev protein and the effect of mutations was evaluated in a Rev nuclear export activity assay (Fig 4A).
Using the same reported mutation and clinical outcome data used in the original publication reporting the TCGA GBM data, we identified IDH1 to be associated with the days to death outcome.
The coalescent age estimates of pan-American haplogroups calculated using the same two mutation rates (A2 19.5 ± 1.3 kya/16.1 ± 1.5 kya, B2 20.8 ± 2.0 kya/18.1 ± 2.4 kya, C1 21.4 ± 2.7 kya/16.4 ± 1.5 kya and D1 17.2 ± 2.0 kya/14.9 ± 2.2 kya) and estimates of population expansions within America (~21-16 ~21-16support the pre-Clovis occupation of the New World.
In each simulation, mutations (either synonymous or nonsynonymous) were randomly distributed across a simulated genome, using the same number of mutations as was detected in our experiment.
These authors also analyzed, using the same approach, other mutations found in the factor V gene: F508C variants in exon 10; and G551D, G542X, and R553X variants in exon 11.
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