Re: [Seqan-dev] Blosum80 Matrix

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Good point!

I refurbished the score and matrix code some while back and am quite sure that I replaced the Blosum matrices with identical copies. However, I have no practical knowledge about BLOSUM and amino acid alignments.

I would be willing to replace the matrix in the library if nobody objects.

Hannes, do you and/or your colleagues have any other remarks on the matrices?

Cheers,
Manuel
________________________________________
From: Hannes Hauswedell [hauswedell@mi.fu-berlin.de]
Sent: Monday, May 21, 2012 9:38 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] Blosum80 Matrix

Hey everyone,

the Blosum80 used internally in seqan is this one:
   http://www.cbcb.umd.edu/confcour/CMSC423-materials/BLOSUM80.txt
which says "Matrix made by matblas from blosum80_3.iij"

However most other references to Blosum80 on the web refer to this one:
   http://www.cs.ucf.edu/courses/cap5937/fall2004/assignment2/BLOSUM80
which says "Matrix made by matblas from blosum80.iij"

They do differ quite a bit. Does anyone know the background? Why was one
chosen over the other?

Regards,
Hannes

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