Figure 3
From: Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores
Example showing base mismatches in an alignment produced by DAFS, R3D Align, and RKalign respectively. (a) The predicted common secondary structure and the alignment produced by DAFS between two pseudoknot structures with PDB IDs 1L2X and 1RNK respectively. (b) The known secondary structures of 1L2X and 1RNK and the alignment produced by DAFS. (c) The known secondary structures of 1L2X and 1RNK and the alignment produced by R3D Align. (d) The known secondary structures of 1L2X and 1RNK and the alignment produced by RKalign. The base_mismatch ratio of DAFS (R3D Align, RKalign, respectively) is 57.14% (67.39%, 27.78%, respectively), where the base_mismatch ratios are calculated using the known secondary structures. RKalign produces the best alignment with respect to the known secondary structures of 1L2X and 1RNK.