Homology used in Blast Algorithm

Brian Osborne bosborne at NATURE.BERKELEY.EDU
Thu Sep 22 16:40:39 EST 1994


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?
>: 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

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?

Thank you for your attention to this matter,


Brian Osborne

Plant Gene Expression Center
800 Buchanan Street
Albany, CA  USA 94710
TEL 510-559-5919
FAX 510-559-5718
bosborne at nature.berkeley.edu







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