[BiO BB] Want to test a custom scoring matrix

[Martin Gollery]

Hi Theodore,

For serious work, I don't recommend this, because you would really have to
recalculate lamba and the gap penalties. For playing around, you can specify
the matrix with -M. The easiest thing to do is to backup BLOSUM62, then save
your test matrix with that name. Sneaky, but I think it will work.

Marty

On 2/17/06, Theodore H. Smith <delete at elfdata.com> wrote:
>
> 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 :)
>
> --
> http://elfdata.com/plugin/
>
>
>
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--
--
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
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