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The best signal to noise ratios and the most reproducible results were achieved using 15-mer with oligo (dT 15 spacer and 50 μM concentrated oligonucleotide probes, with the queried position located towards the center of the probe, printed of super-epoxi-coated slides (experimental conditions detailed in Methods).
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The degree of methylation of each queried CpG position was calculated as a percentage (from 0 100% methylation), and used for calculation of methylation values in Table 1.
For each query position q identified in Step 2, we perform an alignment with the seed S inserted in its corresponding position to generate the final alignments.
The alignment score of SP5 for aligning query
Notably, none of these potentials explicitly take into consideration relevant known mutations at the query position.
Since some sequences in a block may only partially align with the query protein and may not cover the query position, the number of query-position-covering sequences in each block is a different variable and is also considered here.
Syntenic depth refers to the number of syntenic regions identified in a target genome for a given query position.
The ratio of the two (RatioNN) may suggest functional implications of the protein sequences surrounding the query position.
However, during the LOO-neglect, randomly selected mutation occurring at the query position was removed from the training set.
The results indicate that using known ΔΔG values of mutations at the query position improves the accuracy of ΔΔG predictions for other mutations in that position.
During each iteration of the LOO-unseen, a single mutation was kept for testing and the rest of the mutations in the query position were used for training.
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