"normalized" or "centered" BLOSUM62 ?

Question

[luc.moulinier]

Hello,

For testing purposes I need a BLOSUM62 matrix having all elements of the diagonal set to a same value, i.e. all identities are the same. Such matrices exist, I found an old "kind of" PAM250 where all diagonal elements are set to 3.5.

I'm aware the terms "normalized" or "centered" are mathematically incorrect, but I don't know the right one to characterize suc matrix.

Can someone point me to the BLOSUM62 matrix, or give me a way to compute it ? I understood it is not a simple task.

Many thanks ! Luc

Answer 1

[Jean-Karim Heriche]

https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt

EDIT: Source code here

[luc.moulinier]

Thanks for the links, but none of these matrices the diagonal elements set to a same value, i.e. have the same score for identity (A,A) = (R,R).