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We decided to retain the best Q correspondences (in this work we use Q=150), rather than fix a hard threshold for the score, since the score distribution is not constant with respect to different image pairs.
We performed an empirical study to obtain a threshold for the score of unlinked SNPs.
In the analyses we have reported, we did not chose a threshold for the score difference due to a SNP intersecting with a TFBS prediction.
A threshold for the score can be set and patients with scores above or below this threshold will be predicted by the model as potential negative or positive rechallenge cases respectively.
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In order to define a threshold for the scores obtained, we defined an OCT4 motif, based on the targets obtained by the three distinct programs (Fig. 4C).
The mean person location was -0.20 (SD 0.78) indicating adequate targeting as well as distribution of the threshold for the scores of the items patients.
The mean person location was 0.49 (SD 1.24) indicating slightly higher contemplation ability among subjects compared to the items, however with a well distribution of the threshold for the scores.
Clinicians can choose different thresholds for the score according to their treatment objectives for the patients.
Thus, the threshold for the conservation score should be selected in light of gene-specific characteristics.
We set the threshold for the conservation score to 0.70 to select target sites that are conserved in mammals.
All blast results were filtered with an E-10 threshold for the alignment score.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com