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Because the marker data we have for mouse are microsatellites rather than SNPs, we use these microsatellite markers as a surrogate of SNPs for the purpose to demonstrate the utility of the model.
To obtain k kernels for marker data, we need k possibly nested or overlapping subsets of the marker set.
We have performed an extensive haplotype analysis and based on all available marker data we get different genotype information associated with the mutant alleles.
To demonstrate the applicability of the model to any kind of binary marker data, we analyzed a different set of marker data collected by Granovskaia et al. (2010).
To analyze the likelihood model for the autotetraploid marker data, we firstly noticed that the parameter α involves information of allele segregation at the green marker only.
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By performing linkage analysis using the 6,219 marker genotyping data, we mapped 6,197 InDel markers across eight LGs of an inter-specific chickpea genetic map (Table 1, Fig. 4A).
For the BC1N pooled marker data set, we also conducted a G-test (log-likelihood ratio test) using Equation 17.4 as demonstrated in Box 17.1 of Sokal and Rohlf (1995), with the random chromosome model as our null hypothesis.
Based on the phenotype and marker genotype data, we implemented the multiple-interval mapping method for a preliminary genome-wide scan for QTL affecting the multiple categorical phenotype of cell aggregation.
Although we did not detect any expression of the Brachyury mesodermal marker (data not shown), we clearly observed a peak of endothelial gene expression (Cdh5, Tie2, and Icam1; Pecand and Vwf) early in reprogramming.
For comparisons with both biallelic marker and STR data, we condensed our high-resolution data set to make it compatible with those available in published studies.
In the genetic marker data presented here, we cannot distinguish between rare homeologous recombination events causing the loss of one parental genome fragment with replacement from the other fragment, and deletion of one fragment without replacement.
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