> Would you please let me know what's known about how to calculate distance
> between two amino acids based on biochemical properties of the molecules ?
There was a paper about ten years ago from Mohana Rao where he calculated
a distance matrix based on the physical properties of amino acids. It
does not perform as well as PAM or BLOSUM in detecting distant homologies,
but it seems more in line with what you're looking for.
Here's a link to the pubmed entry:
> Additional question then is how to compute distance between two amino acid
> sequencies of equal length that differ from each at several positions.
Ummm... there's been a lot of work in this area. Rost and Schneider's
"Pedestrian guide to analysing sequence databases"
at http://www.embl-heidelberg.de/~rost/Papers/Springer96.html is an
excellent place to start.
I'm not sure what kinds of sequences you're matching, or what kinds of
scores you want, but when I looked at it a couple of years ago, I had
trouble finding sequence database searches on the web that would allow you
to plug in your own similarity matrix. In the end, we had to install our
own version of BLAST.