| m | : | Match |
| DM | : | DayMatrix |
Returns: Match
Synposis: This function computes the alignment with maximum similarity score for the Match m at the PAM distance defined by the DayMatrix DM. It computes a local alignment by applying dynamic programming in a forwards and backwards manner until the score stabilizes. The LogDelLocalRefine function uses a logarithmic deletion cost.
Examples:
> DB := ReadDb('~cbrg/DB/SwissProt'): CreateDayMatrices():
> m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))):
> m := LogDelLocalRefine(m, DM); # compute best local alignment at 250 PAM
> print(m);