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Refine Log

Calling Sequences:
m, DM)
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.


> 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);

Gaston Gonnet