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Using a score cutoff of 50 and expect value of 0.0001, 2358 predicted T. brucei proteins were paired to a human gene (2826 for S. cerevisiae).
Using a score cutoff of 1.9, DrugFEATURE identified all 10 druggable and 13 of the 14 the undruggable sites, with one false-positive prediction.
Using a score cutoff that balances the rate of true positive and false positives in our original two controls, we identified a set of alternatively spliced genes and corresponding exons (see Methods).
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Default settings were used with a score cutoff ≤ 2.5.
The resulting combined alignment was subsequently trimmed with trimAl v1.3 [ 89] using a consistency score cutoff of 0.1667 and a gap score cutoff of 0.9.
Both the focused-set and random-set compounds were docked, and the top hits were selected using a docking score cutoff value equal to the docking score of the native ligand in each crystal structure.
Quality scores were generated for each genotype, using a GenCall50 (GC50) score cutoff of 0.25 and a CallRate (CR) threshold of 0.85.
Thus, the occurrence of chimeric sequences was re-evaluated using a chimera score cutoff of 10 and only 497 ISUs containing 1834 total reads (0.015% of the dataset) were above this threshold.
For survival analysis, TCGA expression data were categorized using a Z score cutoff of 1.0.
The peak lists were initially searched against the NCBI A. mellifera protein database (plus human contaminants and digestion enzymes) using a Mascot score cutoff of 27, essentially as described [ 5].
We determined that using a SPAAT score cutoff of 3 identified 23 patients with complete resection and 4 patients with incomplete resection, for a sensitivity and specificity of 100%%.
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