Homology used in Blast Algorithm

Keith Robison robison at nucleus.harvard.edu
Fri Sep 30 07:57:42 EST 1994

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

: 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?

Look in the BLAST distribution from NCBI.  If you don't feel
like getting the whole thing, I think there is an "explode" 
subdirectory with the file structure laid out.  Look in


The BLAST distribution can be found on


by either FTP or Gopher.

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

robison at mito.harvard.edu 

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