my Profile reply

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Tue May 12 17:44:53 EST 1992

Dear BioNetLanders:

Many thanks extended to all of you who responded last month to my letter
regarding GCG's (via Michael Gribskov) profile analysis method.  I do apologize
for the tardiness of my reply; all standard excuses apply.  Special "Thank
You's" to Don Gilbert who offered his archive site as a depository for my data
(I'll get that README file written and send in my library soon; I promise.) and
EXTRA SPECIAL APPRECIATION to Roland Luethy who sent me the FORTRAN code to
align two profiles to produce a consensus alignment and a new, merged
profile---it appears to work very well!  

As promised, I'm enclosing the list of profiles that I have assembled over the
past couple of years.  I am creating new ones all of the time so it will be
expanded in the future.  I consider these "high quality" profiles although I
have not applied any special statistics to them.  Sandor Pangor offers the
appropriate suggestion to screen them with Student t-value testing, but I have
not taken that step.  I have eliminated all duplicate entries in them,
differentially weighted many of the similar entries, and often trimmed off
highly variable termini.  Additionally, all have been backscreened to the
databases using ProfileSearch and "found" only themselves with "high" Z scores. 
I know, all rather empirical verbage, but they do work well.  The individual
entries' names, weights and beginnings/endings are all listed in the headers to
each profile as per standard GCG format.

If anyone is interested in any of these profiles, please drop me a line and
I'll be happy to send them your way.  Profiles are wider than 80 characters so
MAIL transfers will not work, however if you're on Jnet SEND/FILE/VMSDUMP works
or we can work out an FTP transfer.  I WILL get these into Don's archive to
solve these technical problems but don't hold your breath---I'm REALLY BUSY.

			Thanks again; I hope somebody can use some of this,

						Sincerely, Steve

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                  BITnet:  THOMPSON at WSUVMS1 or STEVET at WSUVM1
                   INTERnet:  THOMPSON at wsuvms1.csc.wsu.edu

The refined profiles assembled by Steven M. Thompson 
as of May 1992 (VMS block size & date also listed):

Insulin-Like Growth Factor II:

IGF2.PRF;1               20  31-OCT-1991
Scrapie/Prion Protein:                          
PRION.PRF;1              67  10-JUN-1991
OVALBUMIN.PRF;1         191  22-FEB-1991
Ribulose Biphosphate Carboxylase/Oxygenase:

ACTIVE_SITE.PRF;3        44  12-NOV-1991
LSU.PRF;2               132   8-NOV-1991
PROLSU.PRF;1            127  13-NOV-1991
G-Protein Linked Receptors:             
NEUROKIN.PRF;1           82   7-FEB-1992
RHODOPSIN.PRF;1         118  25-MAR-1991
HUMAN.PRF;1             159   3-APR-1992
CRF.PRF;1                50  13-FEB-1992
GRF.PRF;1                28  13-FEB-1992
SMS.PRF;1                36  13-FEB-1992
SMS1.PRF;1               33  13-FEB-1992
SMS2.PRF;1               34  13-FEB-1992
TRH.PRF;1                69  13-FEB-1992
AZURIN.PRF;2             35   4-FEB-1992
Phospholipase A2:                       
PA2-1.PRF;1              38  11-MAR-1992
PA2-2.PRF;1              41  11-MAR-1992
PA2-3.PRF;1              37  11-MAR-1992
PA2-CAT.PRF;1            30   8-APR-1992
PA2.PRF;1                48   7-APR-1992
Kazal type protease inhibitor:          
KAZAL.PRF;1              18   7-APR-1992
Apicomplexan antigen protein families:  
APICAL.PRF;1            156   6-MAY-1992
BABR.PRF;1               55   6-MAY-1992
CSP.PRF;1               117  11-MAY-1992
HRP.PRF;1                87  11-MAY-1992
HSP70like.PRF;1          79  11-MAY-1992
KNOB.PRF;1              163  11-MAY-1992
OS25.PRF;1               55  11-MAY-1992
PMMSA-NH.PRF;2          194  11-MAY-1992
PMMSA-CO.PRF;2          237  11-MAY-1992

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