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 is hopelessly out of date.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 Outdated releases don't smell and don't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/
