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The RNAz predictions were assigned genic contexts according to the same criteria as for the homology based annotations.
To achieve stability in the prioritized lists, the algorithm has been trained and tested 200 times, after which the new predictions were assigned by averaging scores.
Multiple univariate OLR models were generated using up to 20 miRNAs with the highest individual concordance values and chemotherapy response predictions were assigned based on the geometric means of multiple OLR model-based predictions.
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Joined and clustered predictions are assigned a combined name e. g., Sox for the Sox2/Sox17 predictions.
Medium and low confidence predictions are assigned to the predictions, which are based on observed residue-residue correspondences between identified homologous proteins.
(V2) VIABLE High confidence for viable mutations (novel codon predictions) is assigned based on codons observed in the expanded library (eg, DENV-1234 codon frequency matrix; Observation O4).
(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).
In fact, unlike previous approaches which employ hundreds of outputs (one for each fuel assembly), only two ANN outputs are employed representing the X- and Y-coordinates (location) of instability; (5) the responses of only a few detectors are employed; (6) a measure of confidence in the prediction is assigned.
The final secondary structure profile of the target sequence was assigned such that, for each residue in the sequence, if the secondary structure prediction by different servers agreed, the consensus of the prediction was assigned as the secondary structure for the residue, otherwise, the secondary structure was left unassigned.
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.
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CEO of Professional Science Editing for Scientists @ prosciediting.com