Dayhoff matrix for protein comparisons??

POSTMASTER at NBRF.GEORGETOWN.EDU POSTMASTER at NBRF.GEORGETOWN.EDU
Thu Mar 4 11:25:45 EST 1993


In message <9303041212.AA07559 at net.bio.net> Sarah Dorazio
(sdorazio at miasun.med.miami.edu) inquires
> I have been using the GCG Gap and Bestfit programs to make
> amino acid sequence comparisons between related proteins.  I
> recently learned that implementing something called
> the"Dayhoff matrix" would be better for this purpose.
> 
> Does anyone know how to use this matrix and where I can find
> it?  I would appreciate e-mail responses since I do not read
> this newsgroup often.

The derivation and uses of the accepted point mutation probability matrices are
described in Chapters 22 and 23 of The Atlas of Protein Sequence and Structure,
vol. 5, supplement 3 (1978), pp. 345-358.  

The following data files are available with the standard PIR distribution or
from the PIR Network Request Server.
  filename    description
  --------    -----------
  AAAM.MAT    McLachlan Alternative Amino Acid Matrix (1971)
  GCM.MAT     Genetic Code Matrix
  MD.MAT      250 PAM Mutation Data Matrix (1978), Unknowns Ignored
  MDM150.MAT  150 PAM Mutation Data Matrix (1978), Unknowns Ignored
  MDM250.MAT  250 PAM Mutation Data Matrix (1978), Unknowns Counted
  SWF250.MAT  250 PAM Swiss Mutation Data Matrix (1992), x10
  SWR250.MAT  250 PAM Swiss Mutation Data Matrix (1992), Rounded

To obtain one of these data files from the Network Request Server, send an
electronic mail message containing a line like
  SEND MDM250.MAT
to either FILESERV at GUNBRF on BITNET or to FILESERV at NBRF.Georgetown.EDU on
Internet.  A list of the currently available files can be obtained by sending
the command
  INDEX
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMAST at GUNBRF.BITNET
                                 POSTMASTER at NBRF.GEORGETOWN.EDU




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