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We note that careful consideration should be taken when aligning large structures. It was noted above that in this case it is best to use an iterative approach, which decreases runtime while maintaining accuracy. Setting a low value of p in the first iteration limits the number of neighborhoods and produces an alignment quickly. This alignment, which is more accurate than the seed alignment used in the first iteration, is used as the seed alignment for the second iteration. Because this seed alignment is more accurate, a smaller bandwidth can be used for the second iteration, which decreases runtime and allows a higher value of p to be set to produce an even more accurate alignment. This iterative approach produces results similar to simply running one iteration with large values of p and β, but it does so in significantly less time. The R3D Align web server allows the user to perform an alignment with up to three iterations automatically.
In this section, we focus on the alignment of the 16S rRNA molecules of E.coli and T.th., PDB files 2avy and 1j5e, respectively (Schuwirth et al., 2005; Wimberly et al., 2000). Because the DIAL and SARA web servers are incapable of producing alignments of structures this large, we asked the authors of the respective programs to provide alignments from local installations of these programs. The R3D Align web server is capable of aligning 16S and even 23S rRNA molecules. Evaluations of the 5S and 23S alignments can be found in Supplementary Materials S4 and S5. 041b061a72