PAM Matrix Visualization

By Ed H. Chi

Hi, Everyone,

Here is a simple visualization of what we talked about. It is a visualization of the PAM Matrices used during similarity computation. This is a simple conceptual model of what could become of it. Color is not used in this animation, and the order of the residue is "as is". That is, the order is whatever order PAM Matrices happens to use.

Here is the movie.

Here is the same movie with edge turned on.

Here is the same movie again with edges only.

Note that frame 1 is pam010, frame 25 is pam250. The X and Y axes has

A R N D C Q E G H I L K M F P S T W Y V B Z X *

X represent a "unknown" residue. The lower left corner is A. The next one is R. There are several things that appear interesting to me. The most notable thing is that the diagonal values changes quite dramatically in some cases. The tallest cone is W in the far right back corner. Watch how it grows taller and taller. There are several other residues that appear to grow, but not as dramatically as W. I'll let you guys make your own interpretations, though.

I hope you have a good mpeg movie player on your machine. If not, click here to get it from the Geometry Center.

In addition, here are the individual GIF files for each PAM matrix: