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With an FDR of 0.01, the mean and the maximal precision of our predictions, defined as the percentage of predicted TFBSs within the ChIP-seq peaks, are 10.7% and 31.9%, respectively.
On the other hand, the mean and the maximal recall of our predictions, defined as the percentage of ChIP-seq peaks with predicted TFBSs among all ChIP-seq peaks with putative binding sites, are 5.0% and 17.1%, respectively.
In our datasets, accurate predictions defined as the correct amino acid type being the most probable reached 89% (Fig. 1c).
The accuracy (AC i ) of i is the proportion of the total number of correct predictions defined as follows: A{C}_i=frac{T{P}_i+T{N}_i}{T{P}_i+T{N}_i+F{P}_i+F{N}_i} (4).
The incorrect predictions defined as | p i − r i| are weighted by the extent of incorrect expression (r max − r i) and added to the Error, i.e. 'penalized'penalized
High quality predictions, defined as unambiguous well-aligned splice junctions and ungapped genomic sequence, were used in the next iteration (TBLASTN, HMM construction, Genewise prediction, hand annotation).
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In step 1, the prediction defined as a the weighted average over the individual predictions x i of every i th expert is computed.
When multiple predictions are present in a exonerate output, only the main prediction (defined as the highest scoring among those overlapping the original input 'superexon') is reported by selenoprofiles.
Accuracy of prediction, defined as the correlation between the GEBV and the true BV, were estimated as the correlation between the GEBV and adjusted phenotypes in the validation population divided by the square root of heritability (Table 2) obtained when analyzing all eight trials together [ 3].
Then, the proportion of successful predictions among all predictions is defined as the precision.
Accuracy is the proportion of correct predictions, and correct topology predictions are defined as by Krogh et al. (2001).
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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