Synposis: Via dynamic programming and the Dayhoff matrix DM, GlobalAlign creates the alignment between sequences m1 and m2 contained in the Match structure m.
The similarity scoring in the dynammic programming is done relative to DM, therefore, the PAM distance of the alignment is the PAM distance of DM.
If the Length1 and Length2 fields of m structure have not been set (ie. they equal 0), GlobalAlign finds the lengths which maximize the score. Note this score is not necessarily the global best score but the score which maximizes the similarity score found by proceeding left to right through m1 and m2 and cutting the right tails (if necessary). If the lengths are defined, GlobalAlign finds the alignment which maximizes the similarity score.
> DB := ReadDb('~cbrg/DB/SwissProt'): CreateDayMatrices(): > m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))): > m := GlobalAlign(m, DM); # compute alignment at 250 PAM > print(m);