Medium and low confidence predictions are assigned to the predictions, which are based on observed residue-residue correspondences between identified homologous proteins.
(V3) VIABLE Medium confidence for viable mutations (novel codon predictions) is assigned to codons that can be constructed from the position frequency matrix from the expanded library and the AA coded for is observed at the corresponding position in synonymous codons or in results from protein sequence/structure homology searches (SeqalSV/StralSV analyses; Observations O5 and O7).
(V4) VIABLE Low confidence for viable mutations (novel codon predictions) is assigned to codons that cannot be constructed from the position frequency matrix from expanded library, but can be predicted based on corresponding AA positions from synonymous codons or SeqalSV/StralSV analyses (Observation O7).
Similarly, to determine if there was a correlation between the findings of Oligo-analysis and Nucleosome Position Prediction, using perl scripts, the corresponding pNO value obtained with the algorithm "Nucleosome Position Prediction" was assigned to each position of the ATAA motif, having again four values for each motif, one per each position.
A viable solution is a sophisticated weighted vote based on the prediction labels assigned to each instance of the relation [ 29].
For BYPASS predictions, the GO terms were assigned to the predictions using the Gene Ontology database directly.
The characteristics ("O0" to "O8") are used to define different "confidence scores" that can be assigned to predictions of the sequence changes that are likely allowable or likely disallowed from a functional standpoint.
The currently proposed seven levels of confidence scores (viable: V1 V4, non-viable: N5 N7) that are assigned to predictions and assessment of possible sequence changes are as follows: (V1) VIABLE Highest confidence for viable mutations is assigned based on codons observed in the reference library (eg, DENV-2 codon frequency matrix; Observation O0).
If the distance to template.A is smaller, a prediction of "subclass A" is assigned to sample S. A prediction of "subclass B" is similarly performed.
Regionally developed and calibrated ground motion prediction equations (GMPE) were assigned to each seismic source (Bernal 2014), thus allowing the consideration of different hazard intensities such as spectral accelerations, peak ground velocity (PGV), and peak ground displacement (PGD).
