The classification included one of 3 mutually exclusive degrees of conservation, in order of decreasing importance: 1) overlap with a UCSC Most Conserved segment, 2) conservation score >0.7, and 3) conservation score >0.3.
Bases were considered highly conserved if their conservation score was greater or equal 2.0 (0.975 quantil of all conservation scores).
The lower the conservation score the more conserved the position is and the higher the conservation score the less conserved the positions is.
Therefore, a long contiguously conserved region would have a high conservation score.
A conservation score, the posterior probability of being in the conserved state, was also calculated.
We set the threshold for the conservation score to 0.70 to select target sites that are conserved in mammals.
The conservation score measures the fractions of 7-mers that are better conserved than the motif, i.e. a conservation score of 1 means that the motif is better conserved than all 7-mers.
Conservation score of the CNCs ranges from 525 to 710 (PhastCons most conserved elements [3]) (Table S1).
DAXX is colored based on the surface conservation score among orthologs aligned in panel (F).
I have further evaluated the range of surrounding hydrophobicity, long-range order, stabilization center and conservation score for the residues that are contributing to cation π interactions.
In ConCavity, the ranking procedure considers overall pocket evolutionary conservation score that is projected onto pocket grid probes.
