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The DrawSimPam Function

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. For example:

> DB := ReadDb('~cbrg/DB/SwissProt'):  CreateDayMatrices():
> m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))):
> m := LocalAlignBestPam( m, DMS ):
> DrawSimPam(m);
The maximum, 275.4, is located at pam=84
The results are contained in Figure [*].

Like all Darwin functions producing graphic files, the results of a DrawSimPam are stored by default in the file in the current directory. Chapter [*] - Randomization, Statistics and Visualization contain a complete description of options and protocols for graphic output.

Figure: The DrawSimPam Function for the Match m. The x axis is the similarity scores while the y axis is the PAM distance.

Gaston Gonnet