From owner-srs@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!sunsite.doc.ic.ac.uk!daresbury!trane.uninett.no!nntp.uio.no!biotek11 From: rodrigol@biotek.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: SRS 4.x on OpenVMS Date: Mon, 03 Jul 95 16:32:39 GMT Organization: Norwegian EMBnet node Lines: 14 Message-ID: <3t8eck$7dg@hermod.uio.no> NNTP-Posting-Host: biotek11.uio.no X-Newsreader: News Xpress Version 1.0 Beta #3 hei Folks, I'm interested in comming in contact with sites that have succesfully installed SRS 4.0x on an OpenVMS box. Anyone out there? R:) ------------------------------------------------------- Rodrigo Lopez The Norwegian EMBnet node Gaustadalleen 21, 0317 Oslo http://biomaster.uio.no ------------------------------------------------------- From owner-srs@net.bio.net Sun Jul 02 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!RRZ.Uni-Koeln.DE!usenet From: "Dr. Joerg Sprengel" Newsgroups: bionet.software.srs Subject: building indices slooow Date: 3 Jul 1995 11:37:05 GMT Organization: Institute of Genetics/Virology Lines: 10 Message-ID: <3t8kp1$o43@news.rrz.uni-koeln.de> NNTP-Posting-Host: gz.genetik.uni-koeln.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; SunOS 4.1.3 sun4m) X-URL: news:bionet.software.srs srsbuild is running since last saturday. I can't remember correctly, but there must be a parameter which restricts the memory requirements. I guess the DECst500/125 with 32Mb PHYSMEM is going to trash (page,swap) the data and no time is left for building the indices.... Any ideas? // Jorg From owner-srs@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!news.sprintlink.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: ANNOUNCEMENT : MAD through SRSWWW Date: 4 Jul 1995 15:19:06 GMT Organization: Belgian EMBnet Node Lines: 19 Message-ID: <3tbm5a$hlo@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] The Malaria Antigen Database is from now on accessible through the Sequence Retrieval System World Wide Webb interface at the site of the Belgian EMBet Node at http://ben.vub.ac.be/srs/srsc It is possible to perform complex queries. E.g. with : falciparum in the Host field bloodstage* in the Expressed field purified in the Production field you would obtain all antigens known to be expressed in the blood stage of Plasmodium falciparum and which have been purified. By clicking on the word MAD you obtain information about the nature of the keywords in the different index tables. SRSWWW retrieves a shortened version of the MAD entries. You can obtain the complete entry by clicking on the MAD ID. From owner-srs@net.bio.net Tue Jul 04 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!bioftp.unibas.ch!ubaclu.unibas.ch!doelz From: doelz@ubaclu.unibas.ch (R.Doelz,Biocomputing Basel;+41 61 267 22 47) Newsgroups: ch.general,bionet.software.srs Subject: CONFERENCE: Biocomputing [CALL FOR PAPERS] Message-ID: <1995Jul5.201435.45122@yogi.urz.unibas.ch> Date: 5 Jul 95 20:14:35 MET Organization: University of Basel, Switzerland Lines: 83 [apologies if you read this more than once] Pacific Symposium on Biocomputing Kohala Coast, Island of Hawaii - January 3-6, 1996 http://cgl.ucsf.edu/psb/psb.html Workshop: Internet Tools for Computational Biology C A L L F O R P A P E R S http://www.ch.embnet.org/psb =============================================================== We would like to invite paper submissions in this exciting field of interdisclipinary research. The development is currently progressing rapidly. In particular, the development of more sophisticated client/server technology to overcome less refined features of the generic http protocol, including authorisation, state, security, synchronisation issues Biological applications start to become indispensible, in particular database retrieval sophisticated program input linkage analysis gene (exon) prediction 3D modelling: MIME types 3D modelling: VRML The most important development 'backstage' is to expand server-server communication for data update and data presentation issues. We welcome papers describing results from a wide range of possible methodologies, including access to, and analyses of the databases of biomolecular sequences and structures, simple conceptual and computational evolutionary models, and success/quality/accessibility reports. Reports on molecular modelling via internet tools and special user group communication, such as MOO interlinking, as well as generic methods for maintenance of information are welcome. Current plans are for electronic publication of the papers by the MIT Press, in both HTML and postscript. People wishing to present posters without publishing a full paper may submit an abstract. Preregistration for the conference is required for the inclusion of a paper in the conference proceedings. IMPORTANT DATES Paper submissions due: July 27, 1995 Notification of paper acceptance: September 11, 1995 Final paper deadline October 2, 1995 Early registration deadline October 2, 1995 More information: Pacific Symposium on Biocomputing Kohala Coast, Island of Hawaii - January 3-6, 1996 http://cgl.ucsf.edu/psb/psb.html Workshop: Internet Tools for Computational Biology http://www.ch.embnet.org/psb =============================================================== R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-srs@net.bio.net Wed Jul 05 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!xlink.net!rz.uni-karlsruhe.de!news.uni-ulm.de!news.belwue.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: SRS 4.x on OpenVMS Date: 6 Jul 1995 10:39:06 GMT Organization: EMBL Heidelberg Lines: 60 Distribution: world Message-ID: <3tgega$erp@comet.EMBL-Heidelberg.DE> References: <3t8eck$7dg@hermod.uio.no> NNTP-Posting-Host: falcon.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX 5.3 IP20) X-URL: news:3t8eck$7dg@hermod.uio.no rodrigol@biotek.uio.no (Rodrigo Lopez) wrote: > >hei Folks, > >I'm interested in comming in contact with sites that have succesfully >installed SRS 4.0x on an OpenVMS box. Anyone out there? > ..seems that there are indeed problems ...probably only on old versions of openvms 1.x ...we have 6.1! i think the problem is in either the file etc/prep_srs.com or etc/srsmake.com they both do a test to find out whether they run on openvms or vax/vms ...the test use different methods this is from prep_srs.com $ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ $ ! find out operating system and define a symbolic name $ ! $ if f$getsyi ("HW_MODEL") .gt. 1024 $ then $ OS_SPECIFIC = "ALPHA" $ else $ OS_SPECIFIC = "VAX" $ endif and this from srsmake.com: $ ! find out whether script is running on an alpha or not $ ! $ if f$getsyi ("ARCH_NAME") .eqs. "Alpha" $ then $ ... $ else $ ... $ endif $ ! i think the latter test is relatively new and might not be supported by old openvms versions ...could you please find out....and mail me the results thure >------------------------------------------------------- >Rodrigo Lopez >The Norwegian EMBnet node >Gaustadalleen 21, 0317 Oslo >http://biomaster.uio.no >------------------------------------------------------- -- =============================================================================== Thure Etzold | EMBL E-mail: etzold@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 387529 | 69012 Heidelberg Fax: (49) 6221 387517 | Germany From owner-srs@net.bio.net Fri Jul 07 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!Germany.EU.net!news.dfn.de!gs.dfn.de!immunbio.mpg.de!immunbio.mpg.de!news Newsgroups: bionet.software.srs Subject: Re: SRS 4.x on OpenVMS Message-ID: <1995Jul7.150652.190@immunbio.mpg.de> From: GARTMANN@IMMUNBIO.MPG.DE (Christoph Gartmann) Date: 7 Jul 95 15:06:51 +0100 References: <3t8eck$7dg@hermod.uio.no> <3tgega$erp@comet.EMBL-Heidelberg.DE> Distribution: world Organization: Max-Planck-Institut fuer Immunbiologie Nntp-Posting-Host: mpi1.immunbio.mpg.de X-News-Reader: VMS NEWS 1.24In-Reply-To: Thure's message of 6 Jul 1995 10:39:06 GMTLines: 28 Lines: 28 In <3tgega$erp@comet.EMBL-Heidelberg.DE> Thure writes: > ..seems that there are indeed problems ...probably only on old versions > of openvms 1.x ...we have 6.1! > > i think the problem is in either the file etc/prep_srs.com or etc/srsmake.com > they both do a test to find out whether they run on openvms or vax/vms ...the > test use different methods Both methods are valid even on VMS 5.5. The problem is with SRSMAKE.COM in that it assumes that on an AXP there is DEC-C and on a VAX it is VAX-C. In the former case the compilation is performed with /STANDARD=VAXC . But in fact there is nowadays DEC-C for VAXen as well. And in this case the above qualifier is required on VAXen, too. In addition I had to deal with the MAKEFILE, at least my version of MAKE for VMS was a bit too restrictive (MMK). Regards, Christoph Gartmann +----------------------------------------------------------------------------+ | Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 | | Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN | | Postfach 1169 Internet: gartmann@immunbio.mpg.de | | D-79011 Freiburg, FRG | +----------- Do you know MENUE, the user environment for OpenVMS? -----------+ From owner-srs@net.bio.net Tue Jul 11 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!Norway.EU.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: What happened to "expression" ? Date: 12 Jul 1995 09:46:01 GMT Organization: Belgian EMBnet Node Lines: 8 Message-ID: <3u05kp$86o@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be. X-Newsreader: TIN [version 1.2 PL2] One of our users noticed that a feature of the WWW interface to GCG has vanished. In the html+ page where you type in a query, there is a "Combine above queries with" followed by a menu with an "expression" item. If you choose this item and you click on "DO QUERY", you however get an empty page. This feature seems to have disappeared when moving from version 4.04 to 4.05 Has someone else noticed the same thing ? From owner-srs@net.bio.net Thu Jul 13 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!xlink.net!rz.uni-karlsruhe.de!news.uni-stuttgart.de!news.belwue.de!news.dfn.de!news.embl-heidelberg.de!usenet From: Thure Etzold Newsgroups: bionet.software.srs Subject: Re: What happened to Date: 14 Jul 1995 17:39:31 GMT Organization: EMBL Heidelberg Lines: 19 Distribution: world Message-ID: <3u6a4j$4om@lion.embl-heidelberg.de> References: <3u05kp$86o@rc1.vub.ac.be> NNTP-Posting-Host: duck.embl-heidelberg.de gbottu@ben.vub.ac.be (Guy Bottu) wrote: > > In the html+ page where you type in a query, there is a > "Combine above queries with" followed by a menu with an "expression" > item. If you choose this item and you click on "DO QUERY", you however > get an empty page. > > This feature seems to have disappeared when moving from version 4.04 to 4.05 > Has someone else noticed the same thing ? you are right ...have to look it up ...i wasn't aware that anybody used that "expression" option;-) thure From owner-srs@net.bio.net Mon Jul 17 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!tank.news.pipex.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!swidir.switch.ch!scsing.switch.ch!ubaclu.unibas.ch!bioftp.unibas.ch!schmitz Newsgroups: bionet.software.srs Subject: Re: SRS 4.x on OpenVMS Message-ID: <1995Jul18.114059.5937@comp.bioz.unibas.ch> From: schmitz@comp.bioz.unibas.ch (Michael Schmitz) Date: Tue, 18 Jul 1995 11:40:59 GMT References: <3t8eck$7dg@hermod.uio.no> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] Lines: 41 Rodrigo Lopez (rodrigol@biotek.uio.no) wrote: : hei Folks, : I'm interested in comming in contact with sites that have succesfully : installed SRS 4.0x on an OpenVMS box. Anyone out there? Hi Rodrigo, hi folks, I am just doing this installation (SRS 4.06, plain distribution) on the Basel URZ cluster, VAX and AXP arch. simultaneously. Besides changes to the sdl files due to the local configuration, I just had to edit makefile.mms to have the executables depend on SRS.OLB instead of SRS.LIB (who has ever seen a .LIB file on VMS?), and to link with sys$library:vaxcrtl.olb/lib (seems Thure forgot the RTL, or the EMBL config links everything with the C libs). The code compiled with no problems - only a single warning, so the srsinstall procedure must have figured out the architecture OK. The local parameters: VAX: VMS 5.5 AXP: OpenVMS 1.5 MMS, no make! The srsbuild procedure is still running (the first attempt crashed with malloc complaining about insufficient memory - I am used to have more wsquota from my time in Duesseldorf), so I don't know if the result of the build makes any sense :-) One question of mine to the masters of the code: My first attempt crashed in the middle of EMBL indexing - and the second one continued building the indices that the first had not written yet. Are the indices written to the time of the crash really complete - or should they be deleted before another attempt (and what about lock files that are checked before continuing)? Regards, Michael Schmitz BioComputing, EMBnet Basel From owner-srs@net.bio.net Mon Jul 17 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!swidir.switch.ch!univ-lyon1.fr!jussieu.fr!oleane!tank.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: Re: SRS 4.x on OpenVMS Date: 18 Jul 1995 12:22:56 GMT Organization: The Sanger Centre Lines: 39 Message-ID: References: <3t8eck$7dg@hermod.uio.no> <1995Jul18.114059.5937@comp.bioz.unibas.ch> NNTP-Posting-Host: unst.sanger.ac.uk In-reply-to: schmitz@comp.bioz.unibas.ch's message of Tue, 18 Jul 1995 11:40:59 GMT In article <1995Jul18.114059.5937@comp.bioz.unibas.ch> schmitz@comp.bioz.unibas.ch (Michael Schmitz) writes: >Rodrigo Lopez (rodrigol@biotek.uio.no) wrote: >: I'm interested in comming in contact with sites that have succesfully >: installed SRS 4.0x on an OpenVMS box. Anyone out there? >I am just doing this installation (SRS 4.06, plain distribution) on the >Basel URZ cluster, VAX and AXP arch. simultaneously. Besides changes to the >sdl files due to the local configuration, I just had to edit makefile.mms >to have the executables depend on SRS.OLB instead of SRS.LIB (who has ever >seen a .LIB file on VMS?), and to link with sys$library:vaxcrtl.olb/lib >(seems Thure forgot the RTL, or the EMBL config links everything with the >C libs). The code compiled with no problems - only a single warning, so >the srsinstall procedure must have figured out the architecture OK. Sounds like you have VAX Fortran and Thure has DEC Fortran. I have been fixing up the same kinds of conflicts for the EGCG code. The fix checks for the DECC compiler using code like the following: $ If ( f$search("sys$system:DECC$COMPILER.EXE").eqs."" ) $ then $! $! must have VAX C (or nothing) $! $ else $! $! DEC C compiler found $! $ endif For EGCG I also have to worry about some of the compiler options between DEC C and VAX C. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England From owner-srs@net.bio.net Tue Jul 18 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!daresbury!bioftp.unibas.ch!schmitz From: schmitz@comp.bioz.unibas.ch (Michael Schmitz) Subject: Re: SRS 4.x on OpenVMS Message-ID: <1995Jul19.172529.22016@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <3t8eck$7dg@hermod.uio.no> <1995Jul18.114059.5937@comp.bioz.unibas.ch> Date: Wed, 19 Jul 1995 17:25:29 GMT Lines: 72 Peter Rice (pmr@sanger.ac.uk) wrote: [discussion about installation of SRS on VMS deleted] : Sounds like you have VAX Fortran and Thure has DEC Fortran. The code is written in Fortran ??? Am _I_ glad ... :-) : For EGCG I also have to worry about some of the compiler options between : DEC C and VAX C. The compiler options stuff had been discussed before (/stan=vaxc/align=whatever), I didn't worry about that. Is there a difference between old DECC and newer versions that have obsoleted to specify the C runtime library on the linker command line ?? Anyway - making a prog depend on something that is never produced by the MMS build procedure must _indeed_ be called a special feature. (Flame off) Seroiusly - to get back to the original question: a) it can be compiled, linked and run under VMS (AXP flavor) b) it produces index files that can be read by getz to do reasonable work (remember Murphy) c) if you run it on a VMS box, be sure you either get _huge_ page file quota and WSQuota - or use srscheck -s 1000 as a fallback :-( Due to quota limitatios in Basel, I had to do all real work in my old lab in Duesseldorf - thanx to the colleagues there - where I needed about 100000 pgflquo on an outdated version of the EMBL database. Does anybody know how the virtual memory requirements scale with database sizes ?? ( the -s 1000 switch even worked at Basel URZ ) Does that answer Rodrigo's question (sorry I'm late with this answer, but I started workin on this just monday afternoon) ?? And let me add a novice's question: we tried to incorporate a embl-to- medline link by adding the following to embl.sdl: ------------------------------------------------------------------------------ #field /gblid=%EMBL_RX_FIELD /itype=key /ftype=@DF_EMBL_MEDLINELINK /idtype=@SRSxSEQID /find="medlineid" /begstr="RX "/nextstr="RX " /relIndexSize=0.5 /isSystem=1 #link /id=%EMBL_MEDLINE /lib1=@EMBL_DB /lib2=@MEDLINE_DB /type=index /field1=@EMBL_RX_FIELD /field2=@MEDLINE_ID_FIELD /idtype1=@SRSxSEQID /idtype2=@ENTRY_ID #srsfield /id=%DF_EMBL_MEDLINELINK /shortname="RX" /name="MedlineLink" /key="K" and to hyperlink.sdl #hyperlink /field=@EMBL_RX_FIELD /parse=embl_medline /parser=@INSERTLINK_PARSER (if that wasn't present before; I don't know) ------------------------------------------------------------------------------ What I got was the following error after gnawing thru the whole database: e__filopenerr, file could not be opened "srsinx:embl_rx" I feel this should tell me something - but what ?? Thanx in advance, Michael Schmitz BioComputing Basel From owner-srs@net.bio.net Thu Jul 20 23:00:00 1995 Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!EU.net!Belgium.EU.net!chaos.kulnet.kuleuven.ac.be!fysiologie-1.med.kuleuven.ac.be!user From: Jan.Eggermont@med.kuleuven.ac.be (Jan Eggermont) Newsgroups: bionet.software.srs Subject: Re: What happened to Date: Fri, 21 Jul 1995 11:13:17 +0100 Organization: Laboratorium voor Fysiologie - KU Leuven Lines: 21 Distribution: world Message-ID: References: <3u05kp$86o@rc1.vub.ac.be> <3u6a4j$4om@lion.embl-heidelberg.de> NNTP-Posting-Host: fysiologie-1.med.kuleuven.ac.be In article <3u6a4j$4om@lion.embl-heidelberg.de>, Thure Etzold wrote: > >you are right ...have to look it up ...i wasn't aware that anybody >used that "expression" option;-) Well, I do use it and I find it a very handy way of searching databases. So if by any chance you can get this expression option to work in the later versions of SRS, I would be very happy. By the way, SRS is a magnificent tool for molecular biologists. Thanks a lot for your efforts. Regards, Jan Eggermont -- Jan Eggermont Jan.Eggermont@med.kuleuven.ac.be Laboratorium voor Fysiologie - KU Leuven Campus Gasthuisberg tel 32-16-34 59 38 3000 Leuven Belgium fax 32-16-34 59 91 From owner-srs@net.bio.net Thu Jul 20 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!biotek11 From: rodrigol@biotek.uio.no (Rodrigo Lopez) Newsgroups: bionet.software.srs Subject: Re: SRS 4.x on OpenVMS Date: Fri, 21 Jul 95 20:40:17 GMT Organization: Norwegian EMBnet node Lines: 35 Message-ID: <3uobu8$9jl@hermod.uio.no> References: <3t8eck$7dg@hermod.uio.no> <1995Jul18.114059.5937@comp.bioz.unibas.ch> <1995Jul19.172529.22016@comp.bioz.unibas.ch> NNTP-Posting-Host: biotek11.uio.no X-Newsreader: News Xpress Version 1.0 Beta #3 To all who have replied to my query: Thanks a million. We managed to succesfully install the software under AXP-OpenVMS 6.1 in Spain this week. We had all sorts of problems getting the software to unpack correctly, but once this was done, the trick (at least for us - and many thanks to Scott Rose and Christoph Gartmann -) was to: 1. In the srsbuild.com file add '/standard=vaxc /noopt' to the compiler flags section. 2. Modify the .mms file so that it correctly puts the .obj files in the bin instead of the src directory. There is no problem with the srs.olb. 3. One very handy utility for VMS sites w/o mms is mmk, which is available from ftp.spc.edu [.macro32.savesets]mmk.zip (Thanks Christoph!). Link, declare a symbol as 'mms' and viola, you have make system support for VMS. 4. It is extremely important to untar the files appropriately under VMS. Everything may seem to compile if you tranferr the files from a UNIX system over ftp with the above instructions but....there is this nasty message.dat file which can make your life a misery! Again, many thanks to all who helped. R:) ------------------------------------------------------- Rodrigo Lopez The Norwegian EMBnet node Gaustadalleen 21, 0317 Oslo http://biomaster.uio.no ------------------------------------------------------- From owner-srs@net.bio.net Mon Jul 24 23:00:00 1995 Newsgroups: bionet.software.srs Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!utnut!utcsri!newsflash.concordia.ca!CC.UMontreal.CA!news From: Srinivasan Jayashree Subject: A newcomer Content-Type: text/plain; charset=us-ascii Message-ID: Sender: news@cc.umontreal.ca (Administration de Cnews) Content-Transfer-Encoding: 7bit Organization: Universite de Montreal Mime-Version: 1.0 Date: Tue, 25 Jul 1995 15:02:22 GMT X-Mailer: Mozilla 1.1N (X11; I; IRIX 5.3 IP19) X-Url: news:bionet.software.srs Lines: 25 Hi there, I am pretty new to this software and sequence searchs basically. However, I would like to take a 17 amino acid sequence that I am interested in and sieve through the database of protein (and/or peptide sequences) to look for similar occurrences. I tried to see if the SRS will be the right place to look and I sorta got lost in its manual pages. Nowhere did I see the feature of sequence comparison. Is this not the right place to look? Am I missing something here? Incidentally I tried to use Fasta and blast programs with the SwissProt and PDB and had very little success. Any suggestions are welcome. Please write to me rather than fill up band width in this news group. Many thanks. ============================================================================= = Jayashree Srinivasan = = Departement de Biochimie Hello :514-343-6111 (X5354) = = C.P.6128 succursale Centre-ville Fax :514-343-2177 = = Universite de Montreal = = Montreal H3C 3J7 = = Canada = ============================================================================= From owner-srs@net.bio.net Tue Jul 25 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!trane.uninett.no!Norway.EU.net!EU.net!howland.reston.ans.net!gatech!newsfeed.pitt.edu!dsinc!ub!acsu.buffalo.edu!cederman From: cederman@cs.buffalo.edu (John D Cederman) Newsgroups: bionet.software.srs Subject: 1/60 of a sec. & Dog on Tacoma Brdg. Date: 26 Jul 1995 12:13:14 GMT Organization: University at Buffalo Lines: 19 Message-ID: <3v5bgq$pla@azure.acsu.buffalo.edu> NNTP-Posting-Host: gagarin.cs.buffalo.edu NNTP-Posting-User: cederman X-Newsreader: TIN [version 1.2 PL2] Here are some Trivia Questions I am trying to figure out. 1. What is the correct one word terminology for 1/60 of a second. 2. Also, what was the name of the dog that die on the Washington State on the Tacoma Bridge. Please either post a responce or please email me at the following address. I only have until midnight tonight to know the answer. cederman@armstrong.cs.buffalo.edu Thanks in advance... -- (?) ====================================================================== o John Cederman (cederman) cederman@cs.buffalo.edu *-|-* :-) But I do have a plan, I just don't know it yet. (-: _/ \_ !________@ (*!#$%*) From owner-srs@net.bio.net Fri Jul 28 23:00:00 1995 Path: biosci!daresbury!nntp-trd.UNINETT.no!Norway.EU.net!EU.net!Germany.EU.net!news.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: A newcomer Date: 29 Jul 1995 16:57:30 GMT Organization: embl Lines: 6 Distribution: world Message-ID: <3vdp9q$jfc@lion.embl-heidelberg.de> References: NNTP-Posting-Host: phenix.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1S (X11; I; IRIX64 6.0.1 IP21) X-URL: news:DCA1s0.HHE@cc.umontreal.ca try http://www.embl-ebi.ac.uk/searches/searches.html Ramu From owner-srs@net.bio.net Mon Jul 31 23:00:00 1995 Path: biosci!daresbury!hgmp.mrc.ac.uk!sanger.ac.uk!pmr From: pmr@sanger.ac.uk (Peter Rice) Newsgroups: bionet.software.srs Subject: SRS reaches 100 databases Date: 01 Aug 1995 08:27:07 GMT Organization: The Sanger Centre Lines: 37 Message-ID: NNTP-Posting-Host: unst.sanger.ac.uk With the addition of the ECOCYC database and the SACCHDB database in several sections each at the Sanger Centre, SRS has now passed the 100 total for databases indexed around the world. ECOCYC is a database of E.coli metabolic pathways from Peter Karp, distributed as 6 flat file sections (E.coli metabolism, compounds, enzyme reactions, genes, pathways and proteins). SACCHDB is a database of budding yeast (Saccharomyces cerevisiae) genome data, distributed as 5 flat file tables (genetic map, locus, ORF, physical map and sequenced regions). More information about these databases is available from the Sanger Centre SRS pages: http://www.sanger.ac.uk/srs/status.html (SRS status page) then click on the "?!" against a database at the Sanger Centre for a description of the data, a link to the original FTP site, and details of search fields and links. To search these databases with SRS: http://www.sanger.ac.uk/srs/srsc where you will find them listed under "Metabolic" and "Genome" libraries. Naturally, as I am still working on the indexing of these databases, the details may change from time to time. -- ------------------------------------------------------------------------ Peter Rice | Informatics Division E-mail: pmr@sanger.ac.uk | The Sanger Centre Tel: (44) 1223 494967 | Hinxton Hall, Hinxton, Fax: (44) 1223 494919 | Cambs, CB10 1RQ URL: http://www.sanger.ac.uk/~pmr/ | England