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For Beagle, we use the default threshold 10E-8.
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The sequences from the ROSETTA design models were aligned and used to build a hidden Markov model using HMMER, the resulting ROSETTA-HMMER model (Rd.HMM for brevity) was calibrated and used to search the NCBI-nr database using the default threshold (E-value smaller than or equal to 10).
To exclude inparalogs, we have used the default threshold score of 0.05.
Neo-epitope prediction was performed with SYFPEITHI using the default threshold (i.e. SYFPEITHI score ≥ 20).
We used the default threshold of 20 summed points for reaching conclusions.
Using the default threshold, we take all candidates with scores above zero as positive interactions.
The threshold cycle (Ct) was determined using the default threshold settings, and the data were analyzed using 2 ΔΔCt program.
The threshold cycle (CT) was determined using the default threshold settings and the data was analysed using the 2 ΔΔCt program.
For IBD-Groupon, using the default threshold (10E-8), the group-wise IBD region was never detected, which is also consistent with the findings of Moltke et al. (2011), which used the default threshold.
All reactions were performed in triplicate, and the Cq values were determined using the default threshold setting.
Using the default threshold, about 29%% (n = 153) of the NFS variants were predicted to be evolutionary intolerant.
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