Homology used in Blast Algorithm

Tim Littlejohn tim at megasun.BCH.UMontreal.CA
Mon Sep 26 10:55:25 EST 1994

In article <199409222140.OAA05470 at nature.Berkeley.EDU> bosborne at NATURE.BERKELEY.EDU (Brian Osborne) writes:
>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?

These can be obtained at NCBI's ftp site:
        anonymous FTP to ncbi.nlm.nih.gov
For the blosum tables, look in the directory /repository/blocks/unix/blosum
For the PAM matricies, there is a program called "pam" which will generate the
tables for you (get pam.c and compile).  This can be found in
/pub/blast/1.4d/explode/blastapp (there are also some PAM tables already
generated; look in the matrix subdirectory).
I hope this helps,

Tim Littlejohn

Tim Littlejohn

E-mail:     tim at bch.umontreal.ca  

Snail Mail: Departement de biochimie        Phone: (514) 343-6111, x5149
            Universite de Montreal          Fax:   (514) 343-2210 
            C.P. 6128, Centre-ville
            Montreal (Quebec), H3C 3J7

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