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. 2015 Feb 6;16:39. doi: 10.1186/s12859-015-0464-9

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© Song et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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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.