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Best Pam Shake

Calling Sequences:
m, DMS)
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.


> DB := ReadDb('~cbrg/DB/SwissProt'):   CreateDayMatrices():
> m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))):
> m := LocalAlignBestPam(m, DMS);
> print(m);

Gaston Gonnet