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.BITNETPOSTMASTER at NBRF.GEORGETOWN.EDU
