Homology used in Blast Algorithm

Keith Robison robison at lipid.harvard.edu
Fri Sep 23 08:09:04 EST 1994

Jonathan Kurtis (Jonathan_Kurtis at Brown.edu) wrote:
: Can someone tell me the exact amino acid assignments used by the Blastp
: program in determining homologies between conservative substitutions?
: Thanks for your help

BLAST lets you pick your substitution matrix; in the case of the 
network/E-mail/WWW servers, you can choose from a set which includes
many PAM and BLOSUM matrices (at different scales) and a handful of others;
if you run BLAST locally you can set up any matrix you want.
The default matrix is the BLOSUM62 matrix generated by Henikoff^2.

Pointers to some relevant literature can be found on the WWW at


Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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