From owner-srs@net.bio.net Sun Jun 01 23:00:00 1997 From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Re: Citation or Reference ? Date: 2 Jun 1997 14:02:46 GMT Organization: Belgian EMBnet Node Lines: 10 Message-ID: <5mujq6$olk@rc1.vub.ac.be> References: <5mkhp5$lb3@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] Path: biosci!rutgers.rutgers.edu!gatech!news1.mid-ga.com!nntp.mid-ga.com!news.oru.edu!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!news-peer.gsl.net!news-dc.gsl.net!news.gsl.net!feed2.belnet.be!news.belnet.be!news.vub.ac.be!ben!gbottu Thure (etzold@ebi.ac.uk) wrote: : there is no real reason for this. Often the name just came from the : description of the data-fields from the databank distribution. : You are right and in SRS they should be called the same - do you : have any preference? I would prefer "Reference" That seems logical to me too. I'll hack the *.i files and put everywhere DF_Reference. From owner-srs@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!Andy.Law From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software.srs Subject: Please help with SRS5 URLs Date: Tue, 03 Jun 1997 10:23:08 +0100 Organization: Roslin Institute Lines: 27 Message-ID: NNTP-Posting-Host: pc0734.ri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.4 I just got round to finishing a program called MacBOB which assists with viewing BLAST and FASTA search results files. Part of what it does is allow the user to retrieve a database sequence reported in the results file by identifying the database alias and sequence ID and then constructing a URL to fling at an SRS server. Unfortunately, it was based on the pre-SRS5 URL syntax, which I notice has just changed. Can someone explain to me the minimal syntax I now need to make this work effectively. Also, have all sites moved over to SRS5 now, or do I need to code preferences for each site (4 versus 5). FYI, I previously used the following syntax http:///srs/srsc?[-id:] substituting , and with the relevant strings. There seem to be a large number of other bits to the URL in version 5 and I'm not sure what they do and which are essential or optional. Any assistance will be gratefully received. TIA Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-srs@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!agate!newsfeed.kornet.nm.kr!news.maxwell.syr.edu!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: Please help with SRS5 URLs Date: 3 Jun 1997 12:48:32 GMT Organization: EMBL Heidelberg Lines: 45 Distribution: world Message-ID: <5n13r0$a4a@lion.embl-heidelberg.de> References: NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) To: Andy.Law@bbsrc.ac.uk X-URL: news:Andy.Law-ya023480000306971023080001@is.bbsrc.ac.uk >Can someone explain to me the minimal syntax I now need to make this work >effectively. Also, have all sites moved over to SRS5 now, or do I need to >code preferences for each site (4 versus 5). > >FYI, I previously used the following syntax > >http:///srs/srsc?[-id:] > >substituting , and with the relevant strings. There >seem to be a large number of other bits to the URL in version 5 and I'm not >sure what they do and which are essential or optional. 1. Individual entry link If the www inteface to srs5 is installed according the installation instruction then you just have to include http:///srs5bin/cgi-bin/wgetz?[database-id:id]+-e for the URL link. This is the minimal syntax. -e flag for displaying the complete entry! Only the has to be changed for all the sites!. 2. Group of entries link Use http:///srs5bin/cgi-bin/wgetz?[dbase-id:id | dbase-id:id]+-newid This will let you go directly into the srs session (query result page). Useful! Hope this helps ! Ramu =============================================================== Chenna Ramu | EMBL E-mail: chenna@embl-heidelberg.de | Postfach 10.2209 Tel: (49) 6221 356229 (Res) | 69012 Heidelberg (49) 6221 387398 (Off) | Germany Fax: (49) 6221 387517 URL: http://www.embl-heidelberg.de/~chenna/ =============================================================== From owner-srs@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!feeder.chicago.cic.net!news.maxwell.syr.edu!news.apfel.de!univ-lyon1.fr!pasteur.fr!jussieu.fr!univ-angers.fr!ciril.fr!u-strasbg.fr!news From: pingouin@crystal.u-strasbg.fr (Francois JEANMOUGIN) Newsgroups: bionet.software.srs Subject: Re: Please help with SRS5 URLs Date: 3 Jun 1997 15:18:50 GMT Organization: IGBMC Lines: 19 Message-ID: <5n1ckq$ofh@news.u-strasbg.fr> References: <5n13r0$a4a@lion.embl-heidelberg.de> <5n19qf$ks8$1@dismay.ucs.indiana.edu> Reply-To: jeanmougin@igbmc.u-strasbg.fr NNTP-Posting-Host: crystal.u-strasbg.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Newsreader: knews 0.9.8 In article <5n19qf$ks8$1@dismay.ucs.indiana.edu>, gilbertd@bio.indiana.edu (Don Gilbert) writes: > Why not continue to support this query link for srs5? > http:///srs/srsc?[-id:] [...] It comes from an old discussion (6 months ago) about problems regarding proxy server. The cgi-bin make the proxy server not to keep this URL. The problem was picked up by someone from infobiogen, if I remmeber well. Check the archive. It's what I understood, correct me if I'm wrong. Francois. -- Francois Jeanmougin | groupe de bioinformatique / bioinformatics groupe tel:(+33) 3 88 65 32 71 | IGBMC BP 163 67404 Illkirch France e-mail : jeanmougin@igbmc.u-strasbg.fr "C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun."(Thiefaine) From owner-srs@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!newsfeed.internetmci.com!in3.uu.net!202.82.1.1!bull.hkstar.net!hkstar2!news From: "=?BIG5?B?qvel1aT0?=" Newsgroups: bionet.software.srs Subject: Help, please Date: 3 Jun 1997 15:22:36 GMT Organization: =?BIG5?B?pL2lcaZXutmlvKq+?= Lines: 3 Message-ID: <01bc702f$fa2c1ca0$LocalHost@default> NNTP-Posting-Host: ip-55-124.dialup.hkstar.com Mime-Version: 1.0 Content-Type: text/plain; charset=BIG5 Content-Transfer-Encoding: 8bit X-Newsreader: Microsoft Internet News 4.70.1157 ½Ð°Ý¦³¨S¦³¤Hª¾¹D¨ºùئ³¤@¨Ç¼sªF¸Ü©Î´¶³q¸Üµo­µªºsoftware¥i¥H download °Ú? ª¾¹Dªº¸Ü, ½ÐÂà§i¤@Án, ÁÂÁ I lookng forward from you soon!! From owner-srs@net.bio.net Mon Jun 02 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!howland.erols.net!vixen.cso.uiuc.edu!news.indiana.edu!not-for-mail From: gilbertd@bio.indiana.edu (Don Gilbert) Newsgroups: bionet.software.srs Subject: Re: Please help with SRS5 URLs Date: 3 Jun 1997 14:30:39 GMT Organization: Biology, Indiana University - Bloomington Lines: 54 Message-ID: <5n19qf$ks8$1@dismay.ucs.indiana.edu> References: <5n13r0$a4a@lion.embl-heidelberg.de> NNTP-Posting-Host: chipmunk.bio.indiana.edu Why not continue to support this query link for srs5? http:///srs/srsc?[-id:] I plan to. It seems cleaner than the one in the default SRS5 and has the great advantange that it is already a standard (other's servers and software like Andy's points to such). Is there software dependent on this srs5 format? http:///srs5bin/cgi-bin/wgetz?[database-id:id] I prefer to change this on my server to something a little simpler, such as http:///srsbin/wgetz?[database-id:id] Is the "5" in srs5 needed for any software? It would seen more maintainable to leave the version number out, to allow for other's links and software to have a standard path (and as I said, I think the srs4 path should be maintained by servers who switch to srs5 to maintain for existing links). For Andy's benefit, this syntax in SRS5 will let one query several databanks: wgetz?[libs={db1 db2 db3}-id:queryterm] or for joint queries: wgetz?[libs={db1 db2 db3}-all:query1]&[libs-org:query2] Are there any better alternate forms of these? Esp. for the multiple Genbank or EMBL "databanks". E.g., I have Genbank, Genbanknew, and GBEST, because they are much easier to maintain separately then as one indexed DB, and european sites have EMBL and EMBLNEW. Is there a simpler syntax to query all the Genbank or EMBL at a site? Something like "[nucleicDB-acc:accessionNumber]" would be nice to support at all srs sites where EMBL or Genbank or DDBJ databanks reside. One problem for my uses has been the spaces in the {db1 db2 db3} list. I'd like to see commas as an alternate delimiter, as in {db1,db2,db3}. To answer another of Andy's questions, I think the switchover to SRS5 will take more time. I've been spending a large chunk of time recently getting the indexing parser (icarus) instructions to work properly for the databanks I support (genbank, pir, some others). Due to limited disk space, I will have to get rid of srs4 soon to make way for srs v5 indices, but other servers may opt to wait until srs 5 indexing details are worked out. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-srs@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!ais.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!newsfeed.internetmci.com!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!serra.unipi.it!bigarea.area.ba.cnr.it!massimo From: Cecilia Lanave Newsgroups: bionet.software.srs Subject: SRS says "No query was specified" Date: Tue, 03 Jun 1997 12:51:32 +0200 Organization: CNR - Area di Ricerca Lines: 8 Message-ID: <3393E8CB.5419@pclanave.ba.cnr.it> Reply-To: cecilia@area.ba.cnrit NNTP-Posting-Host: pclanave.area.ba.cnr.it Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (Win95; I) Will anybody tell me why?? I'm using SRS 5.0 from Bari on Ebi server, and I'm going through this: when submitting any query, mostly using the keyword line, SRS tells me " NO QUERY WAS SPECIFIED ", although an existing keyword was used. Is there anybody out there able to explain me what does this mean? Thank you in advance. areavl21@area.ba.cnr.it From owner-srs@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!server3.netnews.ja.net!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!is.bbsrc.ac.uk!Andy.Law From: Andy.Law@bbsrc.ac.uk (Andy Law) Newsgroups: bionet.software.srs Subject: Re: Please help with SRS5 URLs Date: Wed, 04 Jun 1997 09:41:29 +0100 Organization: Roslin Institute Lines: 23 Message-ID: References: <5n13r0$a4a@lion.embl-heidelberg.de> <5n19qf$ks8$1@dismay.ucs.indiana.edu> NNTP-Posting-Host: pc0734.ri.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.3.4 Thanks to everyone for their help on this. I got a lot of responses and it seems that I will be able to get an SRS5 compatible system up and running without any real trouble. A couple of comments though from a 'user' point of view.. Don, please don't make a unilateral change to SRS addressing at your site. If stuff like my code is to work, then we need ALL the sites to be consistent. I don't care if they all change as long as the changes are consistent at all sites. Could all the SRS site admins who have changed over to srs5 please leave a place-holder/signpost at the old URL to point users across to the new site. I think most have, but the EBI certainly have not. Getting "Document Contains no Data" is not a helpful guide to what has happened to the old service! Thanks again Andy Law ------------------ ( Andy.Law@bbsrc.ac.uk ) ( Big Nose in Edinburgh ) From owner-srs@net.bio.net Tue Jun 03 23:00:00 1997 Path: biosci!CHIPMUNK.BIO.INDIANA.EDU!gilbertd From: gilbertd@CHIPMUNK.BIO.INDIANA.EDU (Don Gilbert) Newsgroups: bionet.software.srs Subject: iubio srs server update and standard SRS server interface Date: 4 Jun 1997 10:12:41 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 103 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706041711.MAA07651@chipmunk.bio.indiana.edu> NNTP-Posting-Host: net.bio.net Thure and SRS service managers, IUBio archive now is running version 5 as its SRS server. The standard link to this is, as it was for version 4, http://iubio.bio.indiana.edu/srs/srsc or http://iubio.bio.indiana.edu/srs/ I would prefer to see SRS servers around the world continue supporting the http:///srs/srsc interface, as it is now a standard link that other molecular biology software and services use. FlyBase uses this, some of my other software does, as does Andy Law's software, and I know that a number of servers use IUBio's SRS server thru this interface. It was always my though that the /srs5/ & /srs5bin/cgi-bin/ links of the new version were just for testing and preliminary deployment. IUBio does offer /srs5/ and /srs5bin/cgi-bin/ as aliases, but as I said in a previous note, I don't think these are necessarily the best choices for a long-term standard interface. Version numbers in it suggest that lots of links will have to change again with version 6. If a new common interface is prefered for version 5, I would vote for something like the plain http:///srs/ and this simple extension for binaries http:///srs/bin/wgetz?whatever or http:///srsbin/wgetz?whatever But I still think the /srs/srsc is better as that (a) already is standard, so no one will need to change links, (b) allows server maintainers to more easily configure just what srsc is, since wgetz is the real name of a program. I use srsc as a script now but will likely change it to an alias for srs/bin/wgetz To support the current standard query "/srs/srsc?query", I've just adapted the old srsc script to add the -e option to cause it to print its data reports, as in "./wgetz -e $*". It should be simple to convert wgetz to do this directly, and avoid an extra process call. Regarding the www-cache technology potential problem, I go along with your analysis, and think the /cgi-bin/ addition is an unneccessary overloading of URL syntax, when there are better server-configurable options available. > From etzold@embl-heidelberg.de Wed Oct 2 17:30:43 EST 1996 > Article: 316 of bionet.software.srs > From: Thure Etzold > Subject: Re: SRS will soon stop working :-) > ... > > Together with Rob Hooft from the EMBL we have looked at that problem in > detail: > > We found alltogether three more or less practical options to turn off > caching: > > 1) include /cgi-bin/ in the URL > 2) adding a 'Pragma:no-cache' header > 3) adding a header with an expiry date, eg, "Expires: Thu, 01 Dec 1994 > 16:00:00 GMT" > > the first we didn't like since it is quite 'clunky' and forces one to > put all cgi's into > a single directory (not just the one of SRSWWW). > > options 2 and 3 both work well ...too well since they turn off cashing > by Netscape > with the consequence that one has to reload always when going a page > back or forward in the > client. > > However, consulting the internet standard RFC 1945 we found this: > > Applications must not cache responses to a POST request because the > application has no way of knowing that the server would return an > equivalent response on some future request. > > Now in SRS5 the pages with user context that are generated by the server > are either POST requests - so they are not cashed - or if obtained by > GET have the user-ID in the URL which makes them unique from pages > retrieved by another user. > > All other page obtained by GET without the userId, eg, pages with single > entries, have no > user context and can be safely cached and shared among users. > > As far as SRS5 is concerned the system should be safe as it is now. > The only page in SRS4 that is problematic is the one with the URL > http://server/srs/srsc > since it contains user context information but the userId is not > included in the URL. > So the best would be to add an expiry date + no cache pragma to the > header of just > that page. > -- Don From owner-srs@net.bio.net Wed Jun 04 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!ais.net!news.maxwell.syr.edu!nntp.uio.no!funny.bahnhof.se!seunet!news2.swip.net!inet-1.pharmacia.se!not-for-mail From: staffan.bergh@eu.pnu.com Newsgroups: bionet.software.srs Subject: range searching in SRS5.0.5 Date: 05 Jun 1997 13:21:53 +0200 Organization: Pharmacia & Upjohn Lines: 17 Message-ID: NNTP-Posting-Host: sgibest.sto.se.pnu.com X-Newsreader: Gnus v5.3/Emacs 19.34 Hi, am I being stupid or ...? Apparently range queries do not work on dates: try the following: getz -f 'dat' '[swissprot-date# 19950101:19950301]' or the equivalent on for instance the EBI SRS server - it returns a lot of entries with no date in the range. In contrast, doing a range query on the SeqLength field works as expected. And yes, the Date field is an integer ... Cheers /staffan ################################################################### Staffan Bergh |Don't let that horse eat that violin Pharmacia & Upjohn, Stockholm | cried Chagall's mother staffan.bergh@eu.pnu.com |but he kept right on painting phone: +46-8-6959884 | (Lawrence Ferlinghetti) From owner-srs@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.internetmci.com!howland.erols.net!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!baron.netcom.net.uk!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: John Peden Newsgroups: bionet.software.srs Subject: getz in SRS5 Date: Fri, 06 Jun 1997 12:41:38 +0100 Organization: Oxford Molecular Biology Data Centre Message-ID: <3397F772.4623@molbiol.ox.ac.uk> NNTP-Posting-Host: udcpc3.jr2.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 3.0Gold (Win95; I) Lines: 63 Hi All Here in Oxford are in the process of migrating to srs5; we are currently running both srs4.08 and srs5.05. One of the primary justifications for duplicating the SRS indexes locally is the ability to use getz for heavy-duty database manipulation, generating specialised blast databases and most importantly in hundreds of scripts to retrieve sequences automatically from or for various analyses. = My problem with srs5 is because the syntax of getz has radically changed; there are 100's of scripts that will break when we migrate. Gratuitous example of srs4 and srs5 getz syntax: SRS4: getz -sf fasta -f "def" -d -l embl -l emnew -l genbank -l genbanknew \ "[sequence-sl#1:] !([sequence-org:metazoa]|[sequence-org:escherich*])"; SRS5.05: getz -sf fasta -f "des seq" \ "[libs=3D{embl emnew genbankgenbanknew}-sl#1:] \ = !([libs-org metazoa]|[libs-org:escherich*])"; = (The outputs are not identical as the srs4 output has an extra = "entry: EMBL:=85.." output field) Has anyone started to or considered writing a wrapper for getz to convert srs4 syntax to srs5? = Is there a general interest in such a wrapper? Are there plans to make SRS5 syntax backwardly compatible thus negating the need for the wrapper? One more question =85 how do you retrieve the annotation part of an entry= using SRS5 getz? I am currently using = SRS4: getz -t '[embl-id:ecreca]' SRS5: getz -sf fasta -e '[embl-id:ecreca]' | sed '/^>/,$ d' I am sure there is a better way ... Many thanks John _____________________________________________________________________ John Peden | johnP@molbiol.ox.ac.uk Molecular Biology Data Centre | Tel. 01865 2-22992 = Oxford University | If its not broke -- then don't fix it ---------------------------------------------------------------------- From owner-srs@net.bio.net Thu Jun 05 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!howland.erols.net!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!baron.netcom.net.uk!netcom.net.uk!server3.netnews.ja.net!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: getz in SRS5 Date: 06 Jun 1997 13:19:21 +0100 Organization: The Sanger Centre Sender: pmr@unst Message-ID: References: <3397F772.4623@molbiol.ox.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 Lines: 34 John Peden writes: > My problem with srs5 is because the syntax of getz has radically > changed; there are 100's of scripts that will break when we migrate. > > Has anyone started to or considered writing a wrapper for getz to > convert srs4 syntax to srs5? > > Is there a general interest in such a wrapper? > > One more question : how do you retrieve the annotation part of an entry > using SRS5 getz? All on my wish list too. At the Sanger Centre I suspect we will have to keep SRS4 running for some of our scripts for a while, though there are so many nice ways to reformat the output in SRS 5 that it should be possible to move many of them without too much effort. certainly the old "-t" and "-d" would be very welcome. So too would the return of the entryname report. Changing "-f def" to "-f des" is another difference that hits our scripts. There are plenty more. But overall, SRS 5 is *so* much nicer. Especially for cross-referencing queries and for customising the database parsing. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: SRS5 Bug in embl Date: Mon, 09 Jun 1997 13:33:47 +0100 Organization: SEQNET Lines: 19 Distribution: bionet Message-ID: <339BF82B.167E@dl.ac.uk> References: <33985ECE.596A@molbiol.ox.ac.uk> <339BC22A.41C6@dl.ac.uk> <339BDED4.4D9C@molbiol.ox.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) The same problem also occurs with swissprot/supdates and genbank/gbonly/gupdates - all cases were different databases share the same syntax. A kludge to make things work (at least on oure site) is to define separate formats and syntaxes for embl and the updates... Not very elegant and I suppose that the srs-team will come with a real solution for this bug. Cheers, Martin -- ----------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/People/m.p.hilbers/ | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | ----------------------------------------------------------------- From owner-srs@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!chippy.visi.com!news-out.visi.com!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: SRS5 Bug in embl Date: 09 Jun 1997 11:27:28 +0100 Organization: The Sanger Centre Sender: pmr@unst Message-ID: References: <33985ECE.596A@molbiol.ox.ac.uk> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 Lines: 50 John Peden writes: > There appears to be a bug in the embl databases under srs5. I have > included an example below ... the problem is present on other sites. It > also appears to be database format (GCG/Native) independent (though the > error message varies between formats). > > > Example > Via the web > select new srs session > select embl and emblnew > use these ID's as your query SMU75476|SMD031 > check the boxes for the three sequences > select save button > select save complete entry = > > select save > > > Errors Messages are: > > www.sanger.ac.uk native embl format = > > says "not possible to write to token table "sequence" I can get this with just SMD031 as the query. Seems to have a problem with retrieving from EMBL and EMNEW. Running wgetz from the command line simply hangs on the second entry. The Sanger Centre message "not possible to write to token table "sequence" is apparently caused by an extra call in embl.is to pick up the entry name ("$Request:entry") inserted by Thure some time back to fix a different problem. On the EBI server, I see no ID for the EMBLNEW entry. The ID is present on the Sanger Centre server. For comparison, the Sanger Centre has EMBL and EMBLNEW indexed in the original flat file version. We made a change to wgetz (with Thure) to fix an EMBL wgetz bu when displaying fields from multiple entries. We also have a fix in embl.is to put an entryname in the header in FASTA format which is needed when the database is in the flatfile version. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!blackbush.xlink.net!news-ge.switch.ch!swsbe6.switch.ch!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: lookup and SRS5 Date: 9 Jun 1997 10:52:11 GMT Organization: Belgian EMBnet Node Lines: 29 Message-ID: <5ngn8r$n22@rc1.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] I am busy finding out if lookup can function with the indexes made by SRS5. I already found that the lookup from GCG 8.1 modified according to Reinhard Doelz can work with indexes made by SRS5. It is however necessary that the environment variable SRSSEC points to a directory containing the files srswin.ptr and srswin.sec from SRS4, because the srs5.ptr and srs5.sec are not compatible. Another problem is that the names of some indexes have changed. The result is that you can e.g. without problem search in Title, but Definition gives nothing. I thought that it might work to change the field definitions in the source code of lookup and recompile. There a terrible problem arose : it has become impossible to compile lookup.c on our computer. Even the code we compiled succesfully in September 1995 can not be recompiled. The reason must be a bug in the Operating system, since we have since then upgraded from OSF/1 version 2 to 4. Hopefully we will soon have egcg9 with a functional elookup. In the meantime the only solution I see is to modify the names of the fields in the Icarus files of SRS5. The only drawback of this would be a lack of consistency with the SRS5 servers on other sites. Other alternatives (keeping two versions of the (bulky) indexes, abandonning lookup, sticking to SRS4) are worse. Anybody a comment ? Guy Bottu this message has also been posted to : bionet.software.gcg From owner-srs@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!europa.clark.net!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: John Peden Newsgroups: bionet.software.srs Subject: Re: SRS5 Bug in embl Date: Mon, 09 Jun 1997 11:45:40 +0100 Organization: Oxford Molecular Biology Data Centre Message-ID: <339BDED4.4D9C@molbiol.ox.ac.uk> References: <33985ECE.596A@molbiol.ox.ac.uk> <339BC22A.41C6@dl.ac.uk> NNTP-Posting-Host: udcpc3.jr2.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Lines: 42 Martin Hilbers wrote: > > > Well.. on our site (http://www.seqnet.dl.ac.uk/srs5) I don't > get an error, but srs does refuse to retrieve an entry with > the same number from both embl and emnew (called eupdates > at our site) Hi Martin Hmmm.... I think the error is still there just you aren't seeing a syntax error, which is what first alerted me. The error is more serious than failing to retrieve an entry with the same number from both embl and emnew. I havn't tested this extensively but in my hands SRS will retrieve a list of embl:* entries or emnew:* entries, but when the list contains embl and emblnew entries the retrieve stops after the last embl entry (none of the emnew entries are extracted). Basically after you have retrieved the three enteries 1 EMBL:SMD031 2 EMBL:SMU75476 3 EUPDATES:SMD031 I can retrieve 1 OK 2 OK 3 OK 1+2 OK 1+3 (fails to return EUPDATES:SMD031) (two SMD031 entries) 2+3 (fails to return EUPDATES:SMD031) (no duplicate entry) 1+2+3 (fails to return EUPDATES:SMD031) I the above on your server just to be sure. I also tested this on the mam division (example: was ID:SM* in the mam division of embl and emnew) john From owner-srs@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!baron.netcom.net.uk!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!lyra.csx.cam.ac.uk!news.ox.ac.uk!news From: John Peden Newsgroups: bionet.software.srs Subject: SRS5 Bug in embl Date: Fri, 06 Jun 1997 20:02:38 +0100 Organization: Oxford Molecular Biology Data Centre Message-ID: <33985ECE.596A@molbiol.ox.ac.uk> NNTP-Posting-Host: udcpc3.jr2.ox.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 3.0Gold (Win95; I) Lines: 65 Hi All There appears to be a bug in the embl databases under srs5. I have included an example below ... the problem is present on other sites. It also appears to be database format (GCG/Native) independent (though the error message varies between formats). Example Via the web select new srs session select embl and emblnew use these ID's as your query SMU75476|SMD031 check the boxes for the three sequences select save button select save complete entry = select save Errors Messages are: www.sanger.ac.uk native embl format = says "not possible to write to token table "sequence" worf.molbiol.ox.ac.uk gcg embl format says syntax error production `seq' : |=E0=D8=FF=FF=FF=FF=FF=FF>>>>SMD031 5/97 2BIT Len: 2195| .....................................^ no match with |^[0-9]+| www.ebi.ac.uk gcg embl format says syntax error production `seq' : | 2195| .....................................^ no match with |^[0-9]+| Via the web select new srs session select embl and emblnew use these ID's as your query SMU75476|SMD031 check all three sequences select save button select save complete entry = select save =46rom the command line: = getz -e '[libs=3D{embl emblnew}-id:SMU75476|SMD031]' Generates an error .... But = getz -e '[libs=3D{ emblnew}-id:SMU75476|SMD031]' getz -e '[libs=3D{embl }-id:SMU75476|SMD031]' work fine ... = john From owner-srs@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!is.bbsrc.ac.uk!news.ox.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Peter Rice Newsgroups: bionet.software.srs,bionet.software.gcg Subject: Re: lookup and SRS5 Date: 09 Jun 1997 14:14:57 +0100 Organization: The Sanger Centre Sender: pmr@unst Message-ID: References: <5ngn8r$n22@rc1.vub.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 Lines: 14 Xref: biosci bionet.software.srs:561 bionet.software.gcg:2545 gbottu@ben.vub.ac.be (Guy Bottu) writes: > Hopefully we will soon have egcg9 with a functional elookup. Sorry. EGCG 9 yes, but elookup with SRS 5 is not possible as far as I can see. My solution is to disable lookup and use getz instead. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Sun Jun 08 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: SRS5 Bug in embl Date: Mon, 09 Jun 1997 09:43:22 +0100 Organization: SEQNET Lines: 67 Distribution: bionet Message-ID: <339BC22A.41C6@dl.ac.uk> References: <33985ECE.596A@molbiol.ox.ac.uk> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) John Peden wrote: > > Hi All > > There appears to be a bug in the embl databases under srs5. I have > included an example below ... the problem is present on other sites. It > also appears to be database format (GCG/Native) independent (though the > error message varies between formats). > > Example > Via the web > select new srs session > select embl and emblnew > use these ID's as your query SMU75476|SMD031 > check the boxes for the three sequences > select save button > select save complete entry > select save > > Errors Messages are: > > www.sanger.ac.uk native embl format > says "not possible to write to token table "sequence" > > worf.molbiol.ox.ac.uk gcg embl format > says syntax error production `seq' : > |àØÿÿÿÿÿÿ>>>>SMD031 5/97 2BIT Len: 2195| > .....................................^ > no match with |^[0-9]+| > > www.ebi.ac.uk gcg embl format > says syntax error > production `seq' : > | 2195| > .....................................^ > no match with |^[0-9]+| > > > From the command line: > > getz -e '[libs={embl emblnew}-id:SMU75476|SMD031]' > > Generates an error .... But > > getz -e '[libs={ emblnew}-id:SMU75476|SMD031]' > getz -e '[libs={embl }-id:SMU75476|SMD031]' > > work fine ... > > john Well.. on our site (http://www.seqnet.dl.ac.uk/srs5) I don't get an error, but srs does refuse to retrieve an entry with the same number from both embl and emnew (called eupdates at our site) Martin -- ----------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/People/m.p.hilbers/ | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | ----------------------------------------------------------------- From owner-srs@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!news.nysernet.net!news-pen-4.sprintlink.net!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!howland.erols.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs,bionet.software.gcg Subject: Re: lookup and SRS5 Date: Tue, 10 Jun 1997 16:51:45 +0100 Organization: SEQNET Lines: 26 Distribution: bionet Message-ID: <339D7811.41C6@dl.ac.uk> References: <5ngn8r$n22@rc1.vub.ac.be> NNTP-Posting-Host: s-ind2.dl.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP12) Xref: biosci bionet.software.srs:564 bionet.software.gcg:2549 Stuart M. Brown wrote: > > Why is ELookup so important? LOOKUP in GCG 9 works fine for me. I want > an EGCG 9 for PRETTYBOX and other functions that are totally lacking > in GCG. > The entire egcg package is important, and we are waiting with moving to gcg 9 until egcg 9 is available. But a version of lookup which can work with the index files of srs is of interest for sites which have both gcg and a SRS server. Otherwise these sites have to do what is essentally the same indexing procedure twice in order to provide the service. Martin -- ------------------------------------------------------------------- | Martin Hilbers http://www.dci.clrc.ac.uk/Person.asp?m.p.hilbers | | SEQNET | E-mail: m.p.hilbers@dl.ac.uk | | Daresbury Laboratory | Tel: +44-1925-603492 | | Daresbury, Warrington | Fax: +44-1925-603100 | | Cheshire WA4 4AD | SEQNET is the UK national EMBNet node | | United Kingdom | http://www.dl.ac.uk/SEQNET/home.html | ------------------------------------------------------------------- From owner-srs@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!128.122.128.2!cmcl2.nyu.edu!news.nyu.edu!mcrcr1.med.nyu.edu!user From: browns02@mcrcr0.med.nyu.edu (Stuart M. Brown) Newsgroups: bionet.software.srs,bionet.software.gcg Subject: Re: lookup and SRS5 Date: Tue, 10 Jun 1997 10:31:29 -0500 Organization: NYU-MC Research Computing Resource Lines: 22 Message-ID: References: <5ngn8r$n22@rc1.vub.ac.be> NNTP-Posting-Host: mcrcr1.med.nyu.edu Xref: biosci bionet.software.srs:563 bionet.software.gcg:2548 In article , Peter Rice wrote: > gbottu@ben.vub.ac.be (Guy Bottu) writes: > > Hopefully we will soon have egcg9 with a functional elookup. > > Sorry. EGCG 9 yes, but elookup with SRS 5 is not possible as far as I > can see. > > My solution is to disable lookup and use getz instead. > ---------------------------------------------------------------------- > Peter Rice | Informatics Division, The Sanger Centre Why is ELookup so important? LOOKUP in GCG 9 works fine for me. I want an EGCG 9 for PRETTYBOX and other functions that are totally lacking in GCG. -- Stuart M. Brown, Molecular Biology Consultant NYU-MC Research Computing Resource, Dept. of Cell Biology 550 First Ave, New York, NY 10016 Phone: (212)263-7689 FAX: (212)263-8139 From owner-srs@net.bio.net Mon Jun 09 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!delos.dra.hmg.gb!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: Peter Rice Newsgroups: bionet.software.srs,bionet.software.gcg Subject: Re: lookup and SRS5 Date: 10 Jun 1997 16:41:17 +0100 Organization: The Sanger Centre Sender: pmr@unst Message-ID: References: <5ngn8r$n22@rc1.vub.ac.be> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.3/Emacs 19.34 Lines: 18 Xref: biosci bionet.software.srs:565 bionet.software.gcg:2550 browns02@mcrcr0.med.nyu.edu (Stuart M. Brown) writes: > Why is ELookup so important? LOOKUP in GCG 9 works fine for me. I want > an EGCG 9 for PRETTYBOX and other functions that are totally lacking > in GCG. It matters if you are running SRS 5.0.5 and do not want to maintain SRS 4.0x with GCG. Hence the demand for a version of LookUp that works with SRS 5.0.5, which SRS servers are rapidly switching to. Sadly, it appears to be beyond the scope of EGCG. It appears to be something GCG would have to implement. -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Tue Jun 10 23:00:00 1997 Path: biosci!rutgers!gatech!csulb.edu!hammer.uoregon.edu!vixen.cso.uiuc.edu!ais.net!newsfeed.internetmci.com!news-was.dfn.de!news-kar1.dfn.de!news-stu1.dfn.de!news.belwue.de!news.uni-ulm.de!not-for-mail From: Markus Kieninger Newsgroups: bionet.software.srs Subject: Problem with Installation of srs5.0.5 on Linux Date: Wed, 11 Jun 1997 17:10:46 +0200 Organization: University of Ulm, Germany Lines: 19 Message-ID: <339EBFF6.3F2D@faw.uni-ulm.de> NNTP-Posting-Host: merlin.faw.uni-ulm.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4c) CC: kieninge Hallo ! I have got a problem with the installation of SRS5.0.5 on a Linux system. After executing the command "srsinstall all" in order to install SRS the installation process stops with the error message "... compiling Icarus files to object base due to error 139". I have installed the same release on a SUN- and IRIX-Workstation without any problems. Can anybody help me with this problem. Markus -- ------------------------------------------------------ Markus Kieninger Tel.: 0731/501-8758 FAW, Ulm E-Mail: kieninge@faw.uni-ulm.de ------------------------------------------------------ From owner-srs@net.bio.net Fri Jun 13 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!swrinde!howland.erols.net!news-peer.gsl.net!news-hk.gsl.net!news.gsl.net!ruby.hknet.com!usenet From: "Vampire" Newsgroups: bionet.software.srs Subject: Bomb Email Date: 14 Jun 1997 10:01:12 GMT Organization: Microsoft Windows 95 Lines: 5 Message-ID: <01bc78a9$dff65440$4cf443ca@hknet> NNTP-Posting-Host: mp329.hknet.com X-Newsreader: Microsoft Internet News 4.70.1157 Hi Everyone, §Ú·Qª¾¥h¨ºùدàdownload¤@¨Ç¥i¥H bomb¤Hemailªºsoftware,¦]¬°§Úµ¹¤Hbomb¤F,©Ò¥H§Ú·Q³ø¤³ ¦pªGª¾¹Dªº,½Ð¦U¦ì¤j¨Ð¯àÁ¿µ¹§Úª¾ Thanks From owner-srs@net.bio.net Mon Jun 16 23:00:00 1997 Path: biosci!daresbury!imbb1.imbb.forth.gr!konops.imbb.forth.gr!maint From: AnoDB updates Newsgroups: bionet.software.srs Subject: Another bug on SRS5 ? Date: Tue, 17 Jun 1997 08:03:27 +0300 Organization: Inst. of Molecular Biology & Biotechnology, Heraklion, Crete, Gr Lines: 17 Message-ID: NNTP-Posting-Host: konops.imbb.forth.gr Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Using SRS5 at EBI I tried to screen EMBL and EMBLNEW for all the sequences containing the string 'Anopheles'. My search returned 824 hits. Then I realized there was no way to fetch them ALL, I had to go over every single sequence and select it. I did it and when I attempted to save them I got a 'server misconfiguration error'. After playing a bit realized that this is the end of every attempt to retrieve more than 300 sequences at once. In order to get the sequences I wanted I decided to get them in parts. I retrieved all the sequences and discovered there were only 758 despite the initial note of 824 hits. P. Topalis From owner-srs@net.bio.net Tue Jun 17 23:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: Another bug on SRS5 ? Date: 18 Jun 1997 12:40:55 GMT Organization: EMBL Heidelberg Lines: 49 Distribution: world Message-ID: <5o8l0n$8mm@lion.embl-heidelberg.de> References: NNTP-Posting-Host: shag.embl-heidelberg.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.12IS (X11; I; IRIX 5.3 IP22) To: chenna X-URL: news:Pine.OSF.3.95.970617075457.31411A-100000@konops.imbb.forth.gr AnoDB updates wrote: > > Hi all, > >Using SRS5 at EBI I tried to screen EMBL and EMBLNEW for all the sequences >containing the string 'Anopheles'. My search returned 824 hits. Then I >realized there was no way to fetch them ALL, I had to go over every single >sequence and select it. Not really! There is a way. Afther the search ... Goto Query manager page. Select the query Click the 'save' buttion You get the Download query page. select the 'use view' as complete entry select the chunk size choose the 'use mime type' to binary so that you can type a file name to save the result. Click the Save button! You are done! Yes, There can be a 'save all' button on the query result page! >I did it and when I attempted to save them I got a 'server >misconfiguration error'. After playing a bit realized that this is the end >of every attempt to retrieve more than 300 sequences at once. >In order to get the sequences I wanted I decided to get them in parts. >I retrieved all the sequences and discovered there were only 758 despite >the initial note of 824 hits. I did not check this. -- ______________________________________________________________ _/_/_/ _/_/_/_/ Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany. _/ _/ _/ Email: chenna@embl-heidelberg.de _/ _/ _/ Url: http://www.embl-heidelberg.de/~chenna/ _/ _/_/_/ Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517 _/ _/ _/ _/_/_/ _/ _/ From owner-srs@net.bio.net Wed Jun 18 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!howland.erols.net!newsfeed.internetmci.com!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: etzold Newsgroups: bionet.software.srs Subject: Re: SRS says "No query was specified" Date: Thu, 19 Jun 1997 18:03:10 +0100 Organization: EMBL-EBI Lines: 18 Distribution: world Message-ID: <33A9664E.31610B00@ebi.ac.uk> References: <3393E8CB.5419@pclanave.ba.cnr.it> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0 [en] (Win95; I) To: cecilia@area.ba.cnrit X-Priority: 3 (Normal) Cecilia Lanave wrote: > > Will anybody tell me why?? > I'm using SRS 5.0 from Bari on Ebi server, and I'm going through this: > when submitting any query, mostly using the keyword line, > SRS tells me " NO QUERY WAS SPECIFIED ", although an existing keyword > was used. this is a known bug in the query form page. This happens when you do a successful query, do a couple of other things and go back (going back in the www client history) to the query page, change the query and submit - for some reason srs then thinks that no query has been specified at all. what you can do at this point is to reload the query form page and then phrase your query. regards Thure From owner-srs@net.bio.net Wed Jun 18 23:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Jun 1997 02:00:05 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199706190900.CAA27842@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-srs@net.bio.net Sun Jun 22 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!vixen.cso.uiuc.edu!ais.net!su-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.nacamar.de!fu-berlin.de!news.belwue.de!news.uni-ulm.de!not-for-mail From: alexander.tress@student.uni-ulm.de (Alexander Tress) Newsgroups: bionet.software.srs Subject: Problems installing SRS 5.0.5 under Linux Date: Mon, 23 Jun 1997 08:12:01 GMT Organization: University of Ulm, Germany Lines: 21 Message-ID: <33ae2d1a.1045263@news.uni-ulm.de> NNTP-Posting-Host: port40-highway.extern.uni-ulm.de X-Newsreader: Forte Free Agent 1.11/32.235 Hello to all, the installation of SRS( call : ./srsinstall all ) is aborted with an 'error 139' during the call to 'srssection'. 'srssection' is a script which consists only of the following call nodd -s $SRSICA/srs.ic $SRSICA/srs.i Calling this from the command-line after preparing the shell with 'source etc/prep_srs.sh' doesn't result in an error, but unfortunately where's also nothing done. Thanks in advance, Alex E-Mail : alexander.tress@student.uni-ulm.de (Alexander Tress) From owner-srs@net.bio.net Mon Jun 23 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: etzold Newsgroups: bionet.software.srs Subject: Re: SRS5 Bug in embl Date: Tue, 24 Jun 1997 15:02:16 +0100 Organization: EMBL-EBI Lines: 35 Message-ID: <33AFD368.D1B7DE2D@ebi.ac.uk> References: <33985ECE.596A@molbiol.ox.ac.uk> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: John Peden X-Priority: 3 (Normal) I found what caused the problem with retrieving entries from both EMBL and EMBLNEW. In general this is true for retrieving entries from more than one databank that share the format object ($libformat). The proper fix for that is rather complicated so i would like to apply the following 'kludge': edit SRSSOU:srs5.h and replace struct LIBoDataType *contains[5]; /* List of types of data contained in the databank described. */ by struct LIBoDataType *contains[4]; /* List of types of data contained in the databank described. */ struct ICAoJOB *job; then edit SRSSOU:entry.c and replace the two occurrences of "lib->job" with "lib->form->job" then recompile srs programs with srsmake regards thure From owner-srs@net.bio.net Tue Jun 24 23:00:00 1997 Path: biosci!rutgers!gatech!howland.erols.net!newsfeed.internetmci.com!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!in2p3.fr!univ-lyon1.fr!pasteur.fr!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: Suggestion Date: Wed, 25 Jun 1997 09:55:03 +0200 Organization: INFOBIOGEN Lines: 17 Message-ID: <33B0CED7.6769@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; SunOS 5.5.1 sun4u) Hello all, I only want to make a suggestion for the future version. Would it be possible put a warning (in the main window for instance) while a bank is not uptodate? that will be better for SRS users to know why sometimes their queries do not work properly. Best regards, Jean-Marc -- --------------------------------------------------- Jean-Marc PLAZA INFOBIOGEN - CNRS 7, rue Guy Moquet BP8 94801 VILLEJUIF Cedex, France tel: +33 45 59 52 39 fax: +33 45 59 52 50 e-mail: plaza@infobiogen.fr --------------------------------------------------- From owner-srs@net.bio.net Tue Jun 24 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: etzold Newsgroups: bionet.software.srs Subject: Re: Suggestion Date: Wed, 25 Jun 1997 12:11:11 +0100 Organization: EMBL-EBI Lines: 17 Message-ID: <33B0FCCF.3150D61D@ebi.ac.uk> References: <33B0CED7.6769@infobiogen.fr> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: Jean-Marc Plaza X-Priority: 3 (Normal) Jean-Marc Plaza wrote: > > Hello all, > I only want to make a suggestion for the future version. > Would it be possible put a warning (in the main window for instance) > while a bank is not uptodate? that will be better for SRS users to > know why sometimes their queries do not work properly. > yes absolutely - i hope to include that in the next version which will appear somewhere in july. Along those lines: i added a new databank "srsupd" on our server at srs.ebi.ac.uk:5000/ which is the srsupdate log file indexed as a databank, this makes monitoring of the automatic update procedure much easier regards thure From owner-srs@net.bio.net Tue Jun 24 23:00:00 1997 Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: etzold Newsgroups: bionet.software.srs Subject: index merge gives error: "message.dat could not be opened" Date: Wed, 25 Jun 1997 12:32:27 +0100 Organization: EMBL-EBI Lines: 15 Message-ID: <33B101CB.F519E92A@ebi.ac.uk> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) CC: Glatting@dkfz-heidelberg.de X-Priority: 3 (Normal) dear all, it has been observed that the command to merge the indices of embl gives an error message like "/data/dat1/srs/etc/message.dat" could not be opened this is caused by the fact that the merge command opens a lot of files simultaneously. On some machines the max. no of files opened by a process (file descriptors) is rather low (eg, 64). use unix command "limit" to find out and "unlimit" to raise that number ...you can have that command into the srsupdate script if you insert it into SRSICA:srsupdate.i regards thure From owner-srs@net.bio.net Wed Jun 25 23:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!newsfeed.direct.ca!ais.net!vixen.cso.uiuc.edu!uwm.edu!fnnews.fnal.gov!nntp-server.caltech.edu!seqaxp.bio.caltech.edu!MATHOG From: mathog@seqaxp.bio.caltech.edu Newsgroups: bionet.software.srs Subject: SRS 5.x, ANSI C compatible? Date: 25 Jun 1997 21:00:56 GMT Organization: Biology Division, Caltech, Pasadena CA 91125 Lines: 25 Message-ID: <5os0u8$had@gap.cco.caltech.edu> Reply-To: mathog@seqaxp.bio.caltech.edu NNTP-Posting-Host: seqaxp.bio.caltech.edu Any progress on a version of SRS 5.x that is ANSI C conformant (and so can be reasonably expected to work on nonUnix systems)? When I tried to build SRS 5.0.5 with DEC C (on OpenVMS, but DEC C on DU would have flagged the same problems), enforcing the ANSI C standard, I ran into a bunch of type conflicts, missing prototypes, and so forth. I worked on cleaning it up for a while, but in the end, gave up when I encountered sections of code that are apparently only meaningful to C++ compilers. Ie, the #ifndef _SDLoOBJ typedef struct SDLoOBJ *dummytointroducestructtagSDLoOBJ; #endif and int OddRegisterObj (SDLoOBJ *obj); constructs (see icaop.c). Thanks, David Mathog mathog@seqaxp.bio.caltech.edu Manager, sequence analysis facility, biology division, Caltech From owner-srs@net.bio.net Fri Jun 27 23:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news.ox.ac.uk!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!news From: etzold Newsgroups: bionet.software.srs Subject: Re: SRS 5.x, ANSI C compatible? Date: Thu, 26 Jun 1997 17:49:21 +0100 Organization: EMBL-EBI Lines: 42 Message-ID: <33B29D91.68F31C6D@ebi.ac.uk> References: <5os0u8$had@gap.cco.caltech.edu> NNTP-Posting-Host: idefix.ebi.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.01 [en] (Win95; I) To: mathog@seqaxp.bio.caltech.edu X-Priority: 3 (Normal) mathog@seqaxp.bio.caltech.edu wrote: > > Any progress on a version of SRS 5.x that is ANSI C conformant (and so can > be reasonably expected to work on nonUnix systems)? > the next version 5.0.6 will be - again - ANSI C conformant. We expect it to be ready about the end of July. The problem at the moment is the C function library that implements the Icarus commands. All these functions lack proper prototypes but they are automatically generated in the new version. > When I tried to build SRS 5.0.5 with DEC C (on OpenVMS, but DEC C on DU > would have flagged the same problems), enforcing the ANSI C standard, I ran > into a bunch of type conflicts, missing prototypes, and so forth. I worked > on cleaning it up for a while, but in the end, gave up when I encountered > sections of code that are apparently only meaningful to C++ compilers. Ie, > the > > #ifndef _SDLoOBJ > typedef struct SDLoOBJ *dummytointroducestructtagSDLoOBJ; > #endif These 'dummies' were also in SRS4 which compiled on openVMS. the problem is that a prototype with an unknown tag, eg, SDLoOBJ like struct SDLoOBJ *myfunct (void); works, however void SDLoOBJ myfunct (struct SDLoOBJ*); gives me warnings about local type definitions, the dummy makes sure that the tag SDLoOBJ is known before the prototype. ...any suggestions to improve that? regards thure From owner-srs@net.bio.net Fri Jun 27 23:00:00 1997 Newsgroups: embnet.general,bionet.software.srs,bionet.immunology Path: biosci!daresbury!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!uranus.ebi.ac.uk!malik From: malik@uranus.ebi.ac.uk (Ansar Malik) Subject: ANNOUNCEMENT: Immunogenetics IMGT database - new release Sender: news@ebi.ac.uk (usenet news) Message-ID: Date: Fri, 27 Jun 1997 15:30:28 GMT Lines: 60 Reply-To: malik@uranus.ebi.ac.uk (Ansar Malik) Organization: European Bioinformatics Institute (EMBL) - UK X-Newsreader: mxrn 6.18-31 Keywords: database, immunogenetics, immunoglobulin, T cell receptor cell,sequences annotation, DNA sequence Xref: biosci bionet.software.srs:607 bionet.immunology:12077 IMMUNOGENETICS IMGT DATABASE =================================== Professor Marie-Paule LEFRANC Laboratoire d'ImmunoGenetique Moleculaire, LIGM UMR CNRS 9942, Institut de Genetique Moleculaire BP 5051, 1919 route de Mende, 34033 MONTPELLIER Cedex 1 FRANCE Telephone: (33) 67 61 36 34 FAX : (33) 67 04 02 31/67 04 02 45 e-mail : lefranc@ligm.crbm.cnrs-mop.fr INTRODUCTION ============ The ImMunoGeneTics database, IMGT, is an integrated specialised database containing nucleotide sequence information of genes important in the function of the immune system. It collects and annotates sequences belonging to the immunoglobulin superfamily which are involved in immune recognition, these are the B cell antigen receptor (Immunoglobulin or Ig), the T cell antigen receptor (TCR) (LIGM-database) and the class I and class II molecules of the Human Leucocyte Antigens (HLA) system (IMGT/HLA-database under development). IMGT/LIGM DATABASE ================== An integrated immumogenetics database (IMGT/LIGM) specialising in Ig and TcR is under development through collaboration between LIGM, IFG and EMBL oustation EBI. This database consists of the Ig and TcR sequence entries. Collaborators: Release 97.06 contains 8622 fully annotated sequence entries. LIGM Montpellier :Marie-Paule Lefranc (coordinator) Veronique Giudicelli,Denys Chaume EMBL-EBI :Ansar Malik IFG :Werner Mueller ACCESS/DATA DISTRIBUTION ======================== SRS server: http://srs.ebi.ac.uk:5000/ NOTE: Selecting this option will bring you to the SRS qerry interface page, where you have to select "search Sequence Libraries" WWW server: http://www.ebi.ac.uk/imgt/ FTP server: ftp.ebi.ac.uk/pub/databases/imgt E_MAIL server: email netserv@ebi.ac.uk -- send "help IMGT" in the mail body. This database is available on CD-ROM as an acompanying database to the EMBL Nucleotide Sequence Database at nominal cost. ======================================================================= Ansar Malik Ph.D | Email:Malik@ebi.ac.uk EBI - European Bioinformatics Institute | URL: http://www.ebi.ac.uk Hinxton Hall, Hinxton | Tel: +44 (1223) 494417 Cambridge CB10 1RQ, UK | Fax: +44 (1223) 494968 ======================================================================== From owner-srs@net.bio.net Sun Jun 29 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!howland.erols.net!newsfeed.internetmci.com!news.wolsi.com!news.aros.net!not-for-mail From: "Chuck Nelson" Newsgroups: bionet.software.srs Subject: Do you need HELP with Hardware Software? Date: 30 Jun 1997 22:14:55 GMT Organization: Free Tech Lines: 6 Message-ID: <01bc8569$fd9fcd60$0c18adcf@chuck> NNTP-Posting-Host: pm1-11.slc.aros.net X-Newsreader: Microsoft Internet News 4.70.1155 Need help with your PC's software and hardware, have a "how to" question. visit the support professionals at Free Tech http://www.free-tech.comDo you need HELP with Hardware Software? From owner-srs@net.bio.net Mon Jun 30 23:00:00 1997 Path: biosci!pravda.ucr.edu!newsfeed2.aimnet.com!europa.clark.net!newsfeed.internetmci.com!in2.uu.net!208.198.64.1!netnews.sbphrd.com!not-for-mail From: Mike Tennant Newsgroups: bionet.software.srs Subject: indexing subdirectiories Date: Tue, 01 Jul 1997 15:18:49 +0100 Organization: SmithKline Beecham Pharmaceuticals Lines: 18 Message-ID: <33B911C9.167E@mh.uk.sbphrd.com> NNTP-Posting-Host: hgu150.ha.uk.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; IRIX 6.2 IP22) Hi, I'm trying to index our pdb hierarchy, which has the format /pdb/dist/*/*.ent.gz, but can't get srs5.05 to get past the first wild card (which is a set of directories). Does anybody know whether this can be done? I have tried the following (and variations) in pdb.i: PDB_FILE:$FileType:[text singleEntry:y maxline:250 saveName:file saveNameLength:20 pipe:"gzcat \%s" searchName:'*\/*.ent.gz' ] thanks in advance! -- Mike. -------------------------------------------------------- Mike Tennant. phone: +44 1279 627866 FAX: +44 1279 627896