[BiO BB] Want to test a custom scoring matrix

[Theodore H. Smith]

Hi people,

I'm just playing around with BLAST to see what it outputs. I figured  
I'd better understand BLAST now as I'm going to have to understand it  
by the end of this project anyhow. (I'm at the beginning of this  
project).

I'm trying to test a made up scoring matrix. It's a very simple one.

#  Here is a matrix I made up.
    A  R  N  D  ...
A  1 -1 -1 -1
R -1  1 -1 -1
N -1 -1  1 -1
D -1 -1 -1  1
...

This is just to get a better idea of how does BLAST work. However, I  
can't figure out how to tell blast to use this matrix file! I don't  
see it in the documentation, although I might have missed something.

Any ideas anyone?

What this experiment is trying to figure out, is does BLAST return  
multiple sections, when doing local alignments. Basically, the same  
quesiton I have before about Smith-Waterman, I was trying to figure  
out how does BLAST work in the same respect. In other words, does  
BLAST match BBBBAAAA to AAAABBBB, to give the alignments:

AAAA
::::
AAAA

and

BBBB
::::
BBBB

I thought I'd figure out the answer myself instead of asking, but I  
couldn't figure out how to input custom scoring matrixes :)

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