[GET-dev] Blosum100 matrix correct in GET?

Xiaodi Wu xiaodi.wu at gmail.com
Tue May 25 14:04:55 EDT 2010

I hadn't looked into it before. Keep in mind that we use the negative
of the BLOSUM value; so we agree on G>A.

As to the other ones, the discrepancy originates in the source data.
The values are in substitution_matrix.py, and the BLOSUM100 there
gives me G>V as -5 and G>R as -4. I got these values from the source
posted at <http://portal.open-bio.org/pipermail/biopython/2000-September/000418.html>
which is in turn derived, for BLOSUM100, from the no-longer
functioning URL
<http://www.embl-heidelberg.de/~vogt/matrices/blosum100.cmp>. I can't
explain why that source gives those values for BLOSUM100. I guess it's
just an inaccurate source, and we can modify it as necessary.

On Tue, May 25, 2010 at 9:10 AM, Alexander Wait Zaranek
<awaitz at post.harvard.edu> wrote:
> I seem to remember you had looked into this.
> ---------- Forwarded message ----------
> From: Kimberly Robasky <krobasky at gmail.com>
> Date: Tue, May 25, 2010 at 10:01 AM
> Subject: [GET-dev] Blosum100 matrix correct in GET?
> To: get-dev at lists.freelogy.org
> I sent this to Tom & Sasha initially, and Xaodi is looking into it,
> but Sasha encouraged me to post it here (where Xaodi can post a response):
> G->A, G->V, G->R in Blosum100 from NCBI are, respectively, -1, -8, -6:
> ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM100
> But on GET, its 1, 5, 4:
> http://evidence.personalgenomes.org/RHO-G51A
> http://evidence.personalgenomes.org/RHO-G51V
> http://evidence.personalgenomes.org/RHO-G51R
> What am I missing?
> -Kim
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