Boundaries determination

Part of the iterative process of building an entry involves trimming the full alignment to produce a new seed alignment for each round, a process which includes boundary determination. Figure 4 shows the difference between the full alignment and the resulting seed alignment after manually assigning boundaries. In Pfam, we adopt a number of different approaches to define the correct boundaries within the alignment:

1. Comparing sequences to known protein structures
2. Building models and altering the boundaries until an optimal solution is found
3. Based on information derived from external resources such as literature and/or experts in the field