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Find Best PAM Distance

Calling Sequences:
m, DMS)
m : Match
DMS : array(DayMatrix)

Returns: Match

Synposis: The Match structure m must contain a resolved match, that is, GlobalAlign, LocalAlign etc. must have been previously executed on m. The FindBestPam function finds the PAM distance which maximizes the similarity score for the alignment contained in m. The results of FindBestPam are dependent on the denseness of the array DMS. The function CreateDayMatrices creates a dense enough array (assigned to DMS) for most practical purposes.


> DB := ReadDb('~cbrg/DB/SwissProt'):   CreateDayMatrices():
> m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))):
> m := LocalAlign(m, DM);           # compute best local alignment at 250 PAM
> m := FindBestPam(m, DMS);
> print(m);

Gaston Gonnet