Plot Pam

Calling Sequences:
DrawSimPam(m)
Parameters:

m

:

Match

Returns: void

Synposis: The function DrawSimPam produces a graph of the similarity score against different PAM distances for a given alignment. This gives the user an intuitive notion of how the similarity changes with changing distances, how precisely defined the maximum is, etc.

By default, the graphics plot is stored in an external file named temp.ps according to the POSTSCRIPT protocol. These default can be changed via the Set command (§).

Examples:

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