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. 2015 Jun 5;43(Web Server issue):W15–W23. doi: 10.1093/nar/gkv543

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© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Schematic representation of Lookup and Data Alignments used by R3D-2-MSA. (A) Lookup Alignment. Sequences from 3D structures (blue) are aligned to the most similar Genbank sequence, the ‘lookup sequence’, shown in black. An inserted sequence (red) is found in this 3D sequence which has no corresponding region in the lookup sequence, shown by the gap in the (black) lookup sequence. The inserted sequence replaces parts of the biological sequence, shown as gaps in the (blue) PDB sequence. (B) Data Alignment. The lookup sequence (black) and five data sequences (green) are shown. The lookup sequence is in both the Lookup and Data alignments and provides the mapping from the PDB sequence positions to the columns of the alignments. Gray dotted lines indicate the positions of gaps and insertions in the lookup sequence in the two alignments.