[BiO BB] PAM vs BLOSUM

[Ryan Golhar]

I started teaching a class and am explainin how PAM and BLOSUM matrices
are derived and how a log-odds matrix works.  

I was wondering if anyone could recommend possible examples to use as
homework questions, or hands-on exercises for students to become aware
of the benefits and differences in the matrices.

I found a Matlab demo that compares the scores of alignments using
different matrices, but it doesn't go to the extent that I was hoping.
If you have any recommendations, I'd love to hear them.  Thanks,

Ryan