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One of the attempts to resolve this problem is proposed in the oPOSSUM system [4], in which three conservation thresholds are linked with the appropriate maximum percentage of conserved regions, ranging from 10% to 30%.
We need the State Water Board to develop permanent mandatory water conservation thresholds, not voluntary targets.
Sequences above certain conservation thresholds were retained for further analysis.
By applying length, %GC and conservation thresholds we have significantly enriched our list of IGRs for known structured RNAs.
These TFBSs are stored in the oPOSSUM-3 database as well as the resulting counts (both single site and cluster sites) for pre-determined conservation thresholds, search region lengths, and profile matrix scoring thresholds.
This explains how in Figure 5B, the number of ortholog sets with 1 to 8 genes that are conserved to 9 reference genes is slightly higher than zero, and likewise for the other conservation thresholds in both Figures 5A and 5B.
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If the conservation threshold is lowered to 90%, then there are still only nine elements conserved between human and frog, five of which overlap with Hox coding sequences.
Consistent with this, amino acid variants in genes not involved in drug resistance fell almost exclusively in less conserved regions with 150 of 153 such amino acid variants below the 2.5 conservation threshold.
Moreover, the phylogenetic footprinting conservation threshold should not be identical for every promoter.
Visualization was done in Jalview, using Zappo colors without conservation threshold, to analyze subgroups [92].
The Conservation threshold parameter is responsible for the elimination of TFBSs with conservation scores lower than the selected threshold.
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