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The remaining 79 originals (79.8%) were inspected with a match percentage of 60.8% (95% CI from 49.1 to 71.6%).
The DNA sequences were aligned using the SeqMan II (DNAstar) and first assembled at a minimum match percentage of 60%, gap lengths 3200, maximum match size 50 bp.
High-stringency assemblies of the viral metagenome were performed using the SeqMan program in the Lasergene software suite (www.dnastar.com/products/lasergene.php) with a minimum overlap of 30 and minimum match percentage of 95%.
The remaining 1037 sequences were assembled into clusters (≥two ESTs) and singletons (one EST) based on the following criteria: sequence match size of 20 bp, minimum match percentage of 85%, 0.00 gap opening penalty, 0.7 gap length penalty, and minimum sequence length of 70 bp.
We performed an initial alignment with a minimum match percentage of 93%.
using default parameters with a minimum match percentage of 95% for sequence assembly.
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This is only marginally better than chance (a matching percentage of 33.3 % is equivalent to someone picking ORS category at random for each video segment).
Overview of measurements comparing the original and reconstructed networks: ratio of overall matches, percentage of correct zeros, percentage of correct ones, and geometrical averages between the two latter percentages expected for random comparisons and obtained from the considered experiments.
A minimum match percentage cutoff of 95% for 40 overlapping bases was used to assign 2 sequences to a cluster.
*Although cases and controls were individually matched, percentages of either are not necessarily equal in each category for sex or area of residence as some cases had one matched control and others had two.
The average pairwise best-matching percentages of the current modules to the previous were obtained at each round of re-clustering, as shown in Additional file 5: Figure S3.
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