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

	blast/matrix/aa

The BLAST distribution can be found on

	ncbi.nlm.nih.gov

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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