[BiO BB] Want to test a custom scoring matrix
Theodore H. Smith
delete at elfdata.com
Fri Feb 17 09:45:11 EST 2006
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
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:
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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