Penalizing Insertions and Deletions in Sequence Alignment

Affine gap penalties

We’ve seen that introducing mismatch and indel penalties can produce more biologically adequate global alignments. However, even with this more robust scoring model, the A-domain alignment that we previously constructed (with indel penalty $σ$ = 4) still reveals only six of the eight conserved purple columns corresponding to the non-ribosomal signatures: