Comparison Tool for Exploring Sequence and Structure Alignments
The Comparison Tool calculates pairwise sequence and structure alignments using different methods. This feature is available on the Compare Structures web page and as a downloadable web widget.
The current sequence alignments possible are blast2seq, Needleman-Wunsch, and Smith-Waterman. Structure alignments can be performed using FATCAT and CE through a Java applet launched from the RCSB PDB site. Mammoth, TM-Align, and TopMatch structure alignments will be launched at their related external sites.
This functionality is also integrated with the Sequence Clusters offered from each entry's Sequence Similarity tab. Users can select a pair of chains from a given sequence cluster, and then run either sequence or structure alignments. For example, the Sequence Similarity tab for entry 4hhb offers sequence clusters at different similarity cutoffs. Users can select a pair of chains from a given sequence cluster (95% for this example), and then run the sequence or structure alignments available from the Comparison Tool.