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Additional SNPs, especially those non-synonymous SNPs in the above mentioned three RGAs, would provide both positional and functional variation sites for further characterization of major gene resistance against C. ribicola.
SNP loci of those candidate genes associated with resistant phenotypes can be used as positional and functional variation sites for further characterization of WWP major gene resistance against C. ribicola.
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The nucleotides from the SNP and InDel variation sites were recorded as marker genotypes for each cultivar.
A discrete-gamma model [53] was implemented to accommodate rate variation among sites for both ML and Bayesian analyses with four different categories.
The extent of rate variation across sites for individual data partitions and for the entire data set was estimated by the shape parameter α of the gamma distribution.
Numerous examples of the importance of incorporating rate variation among sites for the correct phylogenetic inference are found in the literature [ 45– 45].
We detect some variation in polyadenylation sites for transcripts encoded by the three sense/antisense loci (Figure 5 and 6).
This analysis is complicated by the lack of variation at individual sites for sites subject to very strong selection.
It certainly raises the possibility for differences in the highly conserved mechanism of eye development between tephritids and other insects, which might range from control by a distinct gene in Anastrepha, to a variation in binding sites for the P3/RSC1 elements.
The total of 34 significant gene SNPs included 20 and 22 SNPs that were involved in trait variation for site #3 and site #4, respectively, and which were used for association genetic testing; 8 SNPs were detected for the same trait in both sites.
To assess the effects of LCR variations on binding sites for cellular transcription factors, the TFSEARCH software was used [ 16].
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