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In a CM, both the consensus structure of the model and a particular structural alignment of the model to an individual RNA sequence are binary trees.
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80,000 models were generated and the lowest 5% (in full atom energy) were screened against the consensus structure.
The best model for E154 as determined against the consensus structure is shown in Figure 9A alongside the actual active-conformation structure (PDB code: 1ZAO).
For Rio2, the lowest 5% of models were used for screening against the consensus structure as described in the Results section.
The consensus structure shown in Figure 3 represents the typical position of specific and conserved amino acids or amino-acid categories.
Only the score of the consensus structure is given, the structure itself is not shown.
The consensus structure of human RNA structures was then compared to that of mouse one.
The consensus structure is strongly supported by compensatory base substitutions among the Naegleria introns.
We used Weblogo Version 2.8.1 to show the consensus structure of the sequences [ 34, 35].
Then, we fold the sequence constrained with the consensus structure projection (using RNAfold).
We computed the consensus structure of RPS17B and RPS6B introns using Alifold [ 26].
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