Schema of CUSP algorithm and the scoring scheme employed for identifying structurally conserved and unconserved blocks [SSB and USB]. Steps 1–4 illustrate the steps involved in processing structure-based alignments of an example domain superfamily. Scoring schemes that capture structural type exchanges at each position in the alignment (represented as X1 and X2 exchanges for comparisons of each pair) are first applied to each position. Consecutive positions with high scores are merged to identify structurally conserved blocks and distinguish them from indels. An average score is associated with each such block and used to annotate the alignment to distinguish indel regions (USB) from 'core' regions (SSB). In the example, highly conserved structural blocks (H, E and C) identified by high block scores (> 4.5), are indicated in maroon, dark blue and dark green respectively. Conserved blocks that show 'medium' conservation are also indicated (red (helix), cyan (strand) and light green (coil)). The remaining regions are treated as USB.