-+ PROFILES +-

Reinhard Doelz doelz at comp.bioz.unibas.ch
Tue Mar 29 13:29:29 EST 1994


In article <199403281844.AA23124 at wugate.wustl.edu>, brett at BORCIM.WUSTL.EDU writes:
|> Hello. I am interested in programs that will search sequence databases using
|> profiles as query input. I have Macs and Vax, or I could send off my request
|> for remote analysis. We have the GCG PROFILE series of programs, but our db
|> is hopelessly out of date. Any suggestions? Thanx,
|> 

a) URGENT: update your databases. Outdated releases don't smell and don't 
wave at your unaware collagues if they use your site and use these data. 

b) You might want to use the Biocellerator profilesearch mail server which 
was mentioned in the GCG software group before. Rainer Fuch's Mail server 
Utility (as available from EMBL fileserver) has the ability to prepare, 
and format, data in order to be sent to Weizmann. 

c) I have prepared a HASSLE server as Weizmann which accepts input directly; 
a sample output is shown below. HASSLE clients work on most major non-pc 
operating systems. There are also other services, see below. 

Regards
Reinhard 



% profilesearch

   Welcome to the PROFILESEARCH via the network
   (Currently, only Protein searches are supported)
   Please enter the name of your output file 

   ?>test.out 

   The PROFILE service requires that you have created a file 
   of a 'profile' with the program 'profilemake' as distributed 
   by the GCG, Inc. (Genetics computer group). If you don't have 
   the file ready, type 'exit' instead of the filename otherwise 
   type the filename. 

   ?>test.prf

   Please specify the database to use: 

      1) SWISSPROT:*
      2) PIR_INTERNATIONAL:*

   Please enter the appropriate option number :
   ?>1

   Please specify the maximum position-specific gap weight (default=4.5)

   ?>

   Please specify the maximum position-specific gap length weight (default=0.05)

   ?>


      1) Specify more specific parameters
      2) Use defaults 

   ?>2

   Thank you. Preparing datafile... 
--- HASSLE version B4-1-0p (94/03/05) (C) Biocomputing Basel 1992-1994
NOTE: SGBCD.WEIZMANN.AC.IL is used as provider.
NOTE: Listening for reply from SGBCD.WEIZMANN.AC.IL on port 15009 for result
NOTE: Answer from host sgbcd.weizmann.ac.il [132.76.55.13], port 1812 ...Result for service PROFILE 

NOTE: Received file profilesearch_.output 

NOTE: Received file test.out 
NOTE: JOB       15009    completed 




-=-=-=--==-=-=-=-=-= Information on HASSLE  follows =-=-=-=-=-=-=-=-==-=-

Tools are available  which run the following  services;  mostly 
taylored for GCG type of environments. 

	* FASTA (for VAX/VMS) 
		- will do transparent FASTA searching
	* BLAST (all UNIX and VMS except Solaris) 
		- searches with the BLAST algorithm
	* HFETCH (all platforms) 
		- netwide GCG type fetch
	* MEDFETCH (all platforms) 
		- SRS type gateway, will fetch any medline 
		reference (from Entrez) given as swissprot
		entry. Data are searched outside of Entrez.
	* MOWSE (all platforms) 
		molecular weight searching 
	* SWSEARCH (all platforms) 
		smith and waterman type search 
	* PROFILESEARCH_
		profile type searching 

The  following  servers  are  active  at national EMBnet nodes; 
many  thanks  to  all  those  who  volunteered  to have  HASSLE 
providers running: 

	* FRANCE (Solaris) BLAST and HFETCH
	* GREECE (Ultrix) BLAST 
	* ISRAEL (IRIX) SWSEARCH and PROFILE
	* NORWAY (IRIX) BLAST and FASTA 
	* SWITZERLAND (IRIX,AXP/VMS) BLAST,FASTA,HFETCH,MEDFETCH 
	* UK (IRIX) BLAST,MOWSE 

The software and all files are available on nic.switch.ch in the 
mirror/embnet-ch/bioftp-sw/... directories.  The installation is 
straightforward  and  I  would be happy to help anyone who needs 
assistance. 

The load-balancing and fault tolerance was tested with 13 client 
installations operating on 8 servers on wide-area networks. 

The installation of HASSLE at national EMBnet nodes was funded by 
travelling grants from the BRIDGE  Project "Promotion of EMBnet", 
coordinated by Prof. C. Saccone. The  Writing  of HASSLE was sup-
ported by Basel University  and a Grant from the  Swiss  National 
Science Foundation.Hardware support grants from Digital Equipment
and Silicon Graphics are gratefully acknowledged. 


README follows: 
-=-=-=-=-==-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=



         ***********************************************************
         *                                                         *
         *                      H A S S L E                        * 
         Hierarchical Access System for Sequence Libraries in Europe
         *                                                         *
         ***********************************************************


                   V E R S I O N   4 . x   ,    1 9 9 4 

===========================================================================
The HASSLE  protocol  and its associated software modules Customer, Master, 
Responder,  and the local  processing programs ( used collectively with the 
name HASSLE in the following text) in its current Version 4 are copyrighted 
by Biocomputing Basel, and available freely without cost. 

The distribution of the software shall strictly follow the following rules: 
o HASSLE  may  not be sold, as a  whole  or  in  pieces. HASSLE code may be 
    used, adopted,  incorporated in any program package, commercial, share-
    ware or public domain, as long  as the provider of this program package
    makes sure that (a) the HASSLE layer is always up to date with the cur-
    rent HASSLE release version and (b) the incorporation is performed in a 
    fashion that  allows to access the source code, or use HASSLE as provi-
    ded by the original distributor Biocomputing Basel.
o HASSLE may not be used in a  commercial  environment in order to generate 
    profit from services which are accessing the services available via the
    HASSLE protocol. 
o HASSLE may be adopted by  any  service  provider, commercial, non-profit, 
    academic, or  any  other, in the understanding that the provider offers
    services  to the community without charge within the limits of reasona-
    bility. Exceeded limits may not be used as argument to charge  for  the 
    service (see above). 
o HASSLE source code is available for the  current  version  4. In order to 
    keep the communication layer free of trouble,  any  deviation  from the  
    protocol specifications (on port 375) is prohibited. Source code fixes,
    changes, enhancements etc. are most welcome if  documented and communi-
    cated to the  authors. After evaluation, the  changes  will possibly be 
    considered in a new full release version or immediately released as in-
    cremental version if a bug fix is required.  
o HASSLE may be placed on any file server, as long as it is made sure that
    the distribution and documentation are kept up-to-date. 
o HASSLE  customers  and  providers  should always send the registration as 
    distributed with  the  package  in order to be informed and kept up-to-
    date with the development and announcements.
===========================================================================

         ***********************************************************
         *                                                         *
         *                      H A S S L E                        * 
         Hierarchical Access System for Sequence Libraries in Europe
         *                                                         *
         *                                                         *
         * This program package has been written starting from '92 *
         * at the Biocomputing Laboratory, University of Basel, by *
         * Reinhard Doelz. Valuable  suggestions from various col- *
         * leagues, including code contributions (as  documented), *
         * allowed to make this code portable, and  running on the *
         * different platforms.  Though it has been a major effort *
         * to make the HASSLE protocol suite and its  tools  work, *
         * no   responsibility  can   be  taken for  errors  which *
         * might occur while running or result from processing the *
         * program's output. The program writing was supported  by *
         * Basel University, and a grant from the  Swiss  National *
         * Science Foundation (NF). The software resembling HASSLE *
         * may be copied and resdistributed only if this statement *
         * is  preserved.  HASSLE  may not, as a whole or in part, *
         * sold or used by commercial institutions to gain  profit *
         * from the services accessed on the basis of academic re- *
         * search. Users should acknowledge  the  program  package *
         * (Doelz, R., Hierarchical  Access  System  for  Sequence *
         * Libraries in Europe (HASSLE): a tool to access sequence *
         * databases  remotely.  Comput-Appl-Biosci. 10(1), 31-35, *
         * 1994)  if  results  to  be published are obtained.  All *
         * software accessed with the system is copyrighted  sepa- * 
         * rately by corresponding vendors and need to be cited in *
         * publications.                                           *
         ***********************************************************


Thanks: 
To  Ute,  Juergen  and Marianne for the patience; for the funding contribu-
tions  from   Basel  University,  Schweizer Nationalfonds, Silicon Graphics 
and  Digital  Equipment;  and  various suggestions, contributions, and code 
fragments from (alphabetically) K.Adelmann, R.Appel, F.Eggenberger,M.Egger,
J.Epstein,T.Etzold,the whole GCG Team,D.Gilbert,A.Godknecht,M.Hage,R.Harper,
P.Linder,R.Lopez,H.Moeller,R.Omond,F.Roesel,L.Rosenthaler,P.Stoehr,P.Zimak. 

$Id: NOTE.ME,v 1.3 94/02/27 19:04:20 doelz B4-1-0 $








-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=



DISCLAIMER
Note that  the software  mentioned  resembles  Computer  Program(s)  which 
require a license in order to be run unless stated otherwise in  a  state-
ment  codistributed with the software. The use of the program(s) was  men-
tioned  within  a specific problem or example and must not be used to con-
clude that other  software products cannot possibly do a similar job. 




-- 
  +---------------------------+-------------------------------------------+
  |    Dr. Reinhard Doelz     | Tel. x41 61 2672247    Fax x41 61 2672078 |
  |      Biocomputing         | electronic Mail       doelz at urz.unibas.ch |
  |Biozentrum der Universitaet+-------------------------------------------+
  |   Klingelbergstrasse 70   | EMBnet         embnet at comp.bioz.unibas.ch |
  |CH 4056 Basel  SWITZERLAND | Switzerland       gopher.embnet.unibas.ch |
  +---------------------------+------------- http://beta.embnet.unibas.ch/




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