Iterated DDP (cont’d)
In each cycle, only some of the pairs (ai,bj) are used for low level DP
Some pairs, called seeds, are chosen for the first cycle either chosen randomly, or found by a (motif discovery) program (e.g. SPratt)
In each cycle the high level scoring matrix R is updated, and also the selected pairs (ai,bj) for the next cycle
A bias matrix (Q) is used in updating R