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NetPhosK[9] detected 88 of our 91 (97%) candidates as containing Cdk substrates, using a scoring threshold of 0.60− a similar true positive rate as Scansite.
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This evolutionary categorization was repeated using a score threshold of 150 for all databases.
Base calling was performed with phred [ 87, 88] using a score threshold of 20.
Dichotomous classification was performed using a score threshold of 0.65 (patients with scores >/= 0.65 were predicted as cancer-positive and <0.65, cancer-negative).
32 The CDQ showed a sensitivity and specificity of 63.0% and 70.1%, respectively, when using a score threshold of ≥19.5 and 79.7% and 46.8% using a cut-point of ≥16.5.
On the animal data sets, we determined for each of the SBM sets the number of predicted targets obtained by scanning the UTR data set, using a score threshold of 1 [see Additional file 3].
Variation of the costs of the most cost-effective polypill (scenario 2C) showed that when the price of the pill would be under €50 per year (excluding drug delivery costs and including VAT), scenario 2C would become the most favourable scenario when using a SCORE threshold of 7.5%.
We use a score threshold of G T = 0.5 above which we assign GO terms to a wheat gene.
Using a permissive scoring threshold corresponding to the log likelihood score (LLS>0.916) of non-core genome-wide Y2H screens [20], YeastNet v. 2 contains a total of 102,803 linkages covering 5,483 yeast proteins (covering >95%% of validated yeast proteome).
For this reason miRanda was run using a negative score threshold and a positive energy threshold which allowed us to obtain a wide distribution of scores and to ensure consistency.
When using a LOD score threshold of 3 (to match the threshold used in the United Kingdom and Finnish data analyses), we found IBD at a rate of 0.0043.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com