Re: [Seqan-dev] Blosum80 Matrix

[Hannes Hauswedell <hauswedell@mi.fu-berlin.de>]

Hi Manuel,

I have not discussed this with other people and I switched to Blosum62, 
because it was more adequate in the end. It is just something I noticed, 
but maybe you should verify with other people or check which one is used 
by default in other programs...

Best,
Hannes

On 06/05/2012 02:47 AM, Holtgrewe, Manuel wrote:
> 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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