Homology used in Blast Algorithm

micha at amber.biophys.uni-duesseldorf.de micha at amber.biophys.uni-duesseldorf.de
Fri Sep 23 07:33:52 EST 1994

Brian Osborne (bosborne at NATURE.BERKELEY.EDU) wrote:
: Previously :

: >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?
: >
: >Do you need these data sets - or the references given with the BLAST program?
: >Or does BLOSUM / PAM just say it all ??
: >
: >: --
: >: Jonathan Kurtis
: >
: >
: >        Michael Schmitz
: >        Biophysics, Uni Duesseldorf

: I would _very_ much like to know where I can find the actual matrices
: used by these programs, such as BlastP. Once I used "PAM" in a veronica
: search but only found an example of PAM250. Is there a site where these
: might be archived?

Any site running the blast package should have programs to create these.
Blast provides a program to calculate PAM* matrices, and the README for
the package quotes for BLOSUM:
Data repository ncbi.nlm.nih.gov (ftp??), directory /repository/blocks/blosum
_this_ looks like the official archive, if you don't want to bother
Henikoff ..

: Thank you for your attention to this matter,

: Brian Osborne

: bosborne at nature.berkeley.edu

	Michael Schmitz
	Biophysics, Uni Duesseldorf

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