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After mapping, we selected nucleotide sequences from the FL-cDNA locus and CDS of TIGR Pseudomolecules Release 2 to design probes.
After mapping, we selected the reads only mapped to novel exon-exon junctions.
For single-sensor concurrent ratiometric Vm and CaT mapping, we selected dual-excitation/single-emission ratiometric dyes.
Before we performed eQTL mapping, we selected the best RNA-seq run per sample by choosing the run with the highest number of expressed genes.
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With the fine-scale genetic map, we selected 19 contiguous polymorphic SNPs to estimate the age (Table 2).
For building a skeleton map, we selected error-free markers based on the presence of "twins" (i.e., markers with zero distance) in the dataset.
In order to identify the functional similarities among metabolic maps, we selected a subset of nrESS pairwise alignments with score values of ≤0.3.
To reduce the complexity of the interaction maps we selected only the core genes (z-score >2) from the global test analysis (see Additional file 3).
For sequences anchored on the coffee genetic map, we selected a maximum genetic distance of 12 cM between pairs of syntenic markers, which correspond to about 1% of the coffee genetic map (1349 cM).
To represent a QTL on a genetic map, we selected chromosome regions corresponding to a likelihood odds ratio (LOD) greater than the maxmum LOD minus 1, called an LOD-1 interval [ 44].
To start the de novo assembly process of the M. ap ATCC 19698 optical map, we selected the largest ~5% of the optical contigs (larger than 550 kb in length) with average restriction fragment sizes less than 12 kb, and assembled these contigs to form a whole-genome map, termed an "optical consensus map".
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