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While excluding predictions by any method is likely to drop the total number of correctly predicted proteins, we found that when excluding proteins identified by MD this number had shrunk the most (Fig. S3).
This can be used to identify problematic regions in the model, which is more productive than merely accepting or excluding predictions (as in the leverage AD, for example).
For "relaxed" versions that are not intended for direct classification purposes, the accuracy is calculated for Hox genes only (excluding predictions of non-Hox homeobox genes), which under-estimates the global accuracy.
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We also exclude predictions involving proteins that could not be found in any article.
To restrict ourselves to the most novel predictions, we excluded any predictions in which the gene had previously been annotated to any GO term in the same branch as the predicted GO term.
For 205 DUFs, remote relationships could be detected using HHsearch, excluding out predictions for 22 DUF families with dissimilar annotations.
Excluding spurious predictions due to protein misannotation, the following hit was a SirA-like protein that belonged to COG0425 (predicted redox protein, regulator of disulfide bond formation).
The reason for the performance difference between combinations including and excluding "novel" predictions is that AUGUSTUS often reports a transcript with an incorrect first or last exon (i.e. it reports an additional exon, data not shown).
Note that all of these comparative structure prediction methods exclude the prediction of RNA pseudoknots.
In addition, a few predicted values representing the most severe outliers in prediction ability were excluded from prediction error calculation in order to guard against artifactual inflation of the prediction error variance simply due to high collinearity that occasionally occurred in few cross-validations.
We excluded redundant predictions for the same genomic location and only kept the prediction with the highest score.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com