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First, a detailed pair-wise comparison of DIA1 and DIA1R gene products was performed, using amino acid sequence from all species where both genes had been identified (Table S4).
Cpipe supports this requirement by producing three separate reports: a gene level report, an exon level report and a detailed base-pair level gap report.
Note that rough walking direction estimation (leftward vs. rightward) is relatively easily done compared with detailed pair-wise view estimation (30° vs. 45°) required in the generative approaches.
In this study, we provide detailed paired-end read analyses of real sequencing data from two bacteria and generate some useful suggestions for future bacterial genome analyses.
Confirmation of the influence of our screen hits on euchromatin will await a detailed analysis of pairing using FISH probes targeting unique euchromatic sequences.
Notably, most combinations of amino acids in these epistatic sites tend to be associated with CD4+ T cell counts below 500 cells per mm (see Figure 2 for a detailed description of pairs of residues and their correlation with CD4 counts).
Before analysing the diversity components, we selected a subset of environmentally similar paired plots from the Alps and the Scandes using a principal component analysis (PCA) on all six of Ellenberg's indicator factors as well as plot size for all 11,249 plots in the Alps and then added the 481 plots from the Scandes (see Text S1 for a detailed description of the pairing procedure).
A detailed description of mate-pair sequencing is available at http://supportres.illumina.com/documents/myillumina/0a36163e-5fc0-4ae0-a944-a0ee51aa0eb2/matepair_v2_2-5kb_sampleprep_guide_15008135_a.pdf.
Our method produces both a detailed network of significant pair-wise coexpression links and a high-level representation of the modularity in the expression network.
In addition, as per the reviewer's suggestion, we have now added a detailed explanation for CDR3 pair-wise sharing analysis.
We devised a randomization method to identify significant concurrent miRNA-ECs pairs (see a detailed description in Methods).
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