Optimal Alignment Interpretation

Profile-derived alignment score figures for optimal alignments

These bar charts show the optimal profile-derived alignment score for each template residue in the alignment. Gaps relative to the template sequence and any start and end gaps in the alignment are ignored.

Residues Labels

The figure representing the pairwise alignment scores between target sequence and template structure uses the template sequence as residue labels. However, the residue labels for the optimal alignment bar charts are the optimally aligned residues - those residues that will give the highest possible alignment score when aligned with the template structure.

Interpreting the optimal scores

The optimal alignment scores give you an indication of which regions are more conserved in related sequences. So the optimal scores can be used as an aid to interpreting the profile-derived scores for the pairwise alignment. Those regions of a target-template alignment that have poor profile-derived alignment scores may be poorly aligned or it may be that these regions are generally not conserved.