| m | : | Match |
| DMS | : | array(DayMatrix) |
Returns: Match
Synposis: The LocalAlignBestPam alternates between two different optimizations. Given a Match structure, it will call LocalAlign (to improve the local alignment) followed by a call to FindBestPam (to find the best PAM distance) until the similarity score no longer increases.
Examples:
> DB := ReadDb('~cbrg/DB/SwissProt'): CreateDayMatrices():
> m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))):
> m := LocalAlignBestPam(m, DMS);
> print(m);