[BiO BB] BLOSUM matrices

Iddo Friedberg idoerg at burnham.org
Sun Jul 17 22:41:13 EDT 2005

Hi Raj,

Actually, the BLOSUM matrices are constructed based on sequence
alignments, not on structures. More specifically, they are based on the
alignments in the BLOCKS database.


However, going there I could not find updated BLOSUM matrices, although
the BLOCKS is being updated.

You should probably email the BLOCKS folks for updated matrices.
It would be interesting to see if there is any significant difference
between old and new BLOSUM matrices. Although there is an ongoing
explosion in the number of sequences that we have, the statistics of teh 
composition of aligned positions doe snot seem to have changed



Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171

On Sun, 17 Jul 2005, Raj wrote:

>  Hi all,
>     I was wondering if there are latest BLOSUM matrices somewhere. The 
>  matrices in NCBI website are like 8 years old. May be my understanding 
>  is limited but, do the scoring matrices change as new structures are 
>  being solved and added to the database?
>  Regards,
>  Raj
> ===================================
> Rajkumar Bondugula
> Digital Biology Laboratory
> University of Missouri-Columbia
> http://digbio.missouri.edu/~raj
> ===================================
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