Homology used in Blast Algorithm

micha at amber.biophys.uni-duesseldorf.de micha at amber.biophys.uni-duesseldorf.de
Thu Sep 22 15:48:03 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

BlastP (as supplied for complementing the GCG suite) uses the BLOSUM62
matrix as default (but many other BLOSUM* or PAM* data files are available).

Do you need these data sets - or the references given with the BLAST program?
Or does BLOSUM / PAM just say it all ??

: -- 
: Jonathan Kurtis

: International Health Institute
: Brown University Box G-8033
: Providence, RI  02912

	Michael Schmitz
	Biophysics, Uni Duesseldorf




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