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The resulting alignment that can be derived from the collapsed DFMs (A) is compared to the alignments derived from the Dali (B) and Needleman-Wunsch (NW) algorithms (C). Identical pairs are indicated by blue boxes. The single match score (SMS) is depicted underneath the DFM and NW alignments. It can be seen that the region corresponding to the second alpha helix in the NW alignment gives negative SMS values indicating that the dynamic similarity is not preserved in this region.
