my profiles are now available via anon ftp

Steve Thompson: VADMS genetics THOMPSON at WSUVMS1.CSC.WSU.EDU
Thu May 28 10:59:14 EST 1992


Greetings NetLanders and "Profilelers"

Thank you so much for the encouraging words of support and gentle prodding to
get my profiles available for transfer.  I do apologize for the amount of time
it has taken me to get to this point, but you all know the story, busy, busy! 
As promised, I have moved them to a location accessable by anonymous ftp.   I
have not yet documented the profiles and, therefore, have not yet sent them off
to IUBIO.  But in the interest of availability and convenience for everyone I
have placed them in our own VAX cluster's anonymous account.  As for their
full documentation, Michael Gribskov suggests that eventually profiles should
include the multiple sequence alignment and database name entries used to form
them, annotated functional sites, search statistics and literature references. 
A laudable goal indeed, but an incredible amount of work!  One problem I
immediately surmise is that many of my profiles' multiple sequence alignments
are quite huge because of a very large number of entries (e.g. Phospholipase A2
has 91 unique entries).  I could easily append the two files together, .MSF and
.PRF, but do people really want such huge files?  This would be a good topic of
discussion in the newsgroup.  Regardless, my profiles are now available.

I consider these "high quality" profiles although I have not applied any
special statistics to them.  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,
with the obvious exception of families wich are already known to be very
similar to another (such as the Apicomplexan HSP70like antigen profile).  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.

The directory structure and logon information for our anonymous account
follows.  The MolBio directory is empty other than my profiles but we decided
to set it up that way to leave the potential for expansion.  Everyone is
welcome to use my profiles; I only ask that you acknowledge me as their author
and inform me if you publish something which uses them.  I will be expanding
the list in the coming months, so you may wish to check again in the future. 
Again, thanks for all of the support; I hope they can be of some use to you.

							Steve Thompson

********************************************************************************

Internet address:	bobcat.csc.wsu.edu	134.121.1.1
         alias:		wsuvms1.csc.wsu.edu

logon as: 		USER ANONYMOUS
password:               your Internet address

********************************************************************************

path: root/molbio/profiles	(however, this is a VMS site not Unix!)

DIR [ANONYMOUS.MOLBIO.PROFILES]

APICOMPLEX.DIR	AZUZIN.DIR	GRWTHFCTR.DIR	NEUROPEP.DIR	OVALBUMIN.DIR
PHOSPHOLIP.DIR	PRION.DIR	PROTEAINHIB.DIR	RECEPT.DIR	RUBISCO.DIR

and README.TXT (this file)

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

[.APICOMPLEX] 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;2          80  27-MAY-1992
KNOB.PRF;2              116  27-MAY-1992
OS25.PRF;1               55  11-MAY-1992
PMMSA.PRF;1              91  27-MAY-1992
                                        
[.AZURIN] Azurin:                                 
                                        
AZURIN.PRF;2             35   4-FEB-1992

[.GRTHFCTR] Growth Factors and Cytokines:

IGF2.PRF;1               20  31-OCT-1991
                                        
[.NEUROPEP] Neuropeptides:                          
                                        
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
                                        
[.OVALBUMIN] Ovalbumin:                              
                                        
OVALBUMIN.PRF;1         191  22-FEB-1991

[.PHOSHOLIP] Phospholipases:                       
                                        
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

[.PRION] Scrapie/Prion Protein:                          
                                        
PRION.PRF;2              67  27-MAY-1992
                                        
[.PROTEAINHIB] protease inhibitors:          
                                        
KAZAL.PRF;1              18   7-APR-1992
                                        
[.RECEPT] G-Protein Linked Receptors:             
                                        
HUMAN.PRF;1             159   3-APR-1992
NEUROKIN.PRF;1           82   7-FEB-1992
RHODOPSIN.PRF;1          89  21-MAY-1992
                                        
[.RUBISCO] 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
                                        
********************************************************************************

                              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

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