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amino acid identity and similarity matrices

Rosemarie Swanson rosmar at bioch.tamu.edu facil at bioch.tamu.edu
Fri May 14 23:16:00 EST 1993


In article <1993May12.091226.13652 at ac.dal.ca>, jrbrown at ac.dal.ca writes...
>I am interested in a DOS or MAC based program which
>will output a matrix of %identical or % similar amino
>acid positions of multiple aligned sequences. ...
>I have yet to find a program which will simply score the number
>of identical aa positions or similar aa positions (ie. Ileu, Leu
> and Val are similar but not identical).  
> 
>Jim Brown>Dept. of Biochemistry>Dalhousie University>Halifax, N.S.
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I have a small program, "PERCE", (PERCEnt) to produce such matrices -- both
% identical positions and % similarity.  (% similarity is based on the new
"Dayhoff-type mutation data matrix" published in Science 256 1443-5 (1992)
by Gonnet, Cohen and Benner).  It reads GCG-style *.MSF (multiple
sequence alignment files), is in fortran. It runs on a vax, however, not
a PC or Mac.  You are welcome to the source code.  Alternatively, or in
addition, I would be happy to process your aligned sequences through
it for you, if you don't have access to a fortran compiler/and or a vax.

Rosemarie Swanson, Biochem/Biophys, Texas A&M, 409-845-6840



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