From owner-srs@net.bio.net Sun Feb 01 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.gip.net!news-raspail.gip.net!news.gsl.net!gip.net!eerie.fr!jussieu.fr!infobiogen.fr!newsmaster From: Jean-Marc Plaza Newsgroups: bionet.software.srs Subject: links in srs5 Date: Mon, 02 Feb 1998 11:21:51 +0100 Organization: INFOBIOGEN Lines: 69 Message-ID: <34D59E3F.B48EA28D@infobiogen.fr> NNTP-Posting-Host: lovelace.infobiogen.fr Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="------------43F9D54019A253BDEE0C8C8F" X-Mailer: Mozilla 4.04 [en] (X11; I; SunOS 5.5.1 sun4u) CC: etzold@ebi.ac.uk --------------43F9D54019A253BDEE0C8C8F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear srs administrator, I found a problem of making links between databanks with wgetz from srs5.1.0 The error message from the web (error.log) is : [Mon Feb 2 11:04:14 1998] access to /env/infobiogen/pack/srs5/www/bin/wgetz failed for lovelace.infobiogen.fr, reason: Premature end of script headers We work on Sun Solaris 2.5 Sparc SUNW,Ultra-Enterprise 4000 Need help 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 --------------------------------------------------- --------------43F9D54019A253BDEE0C8C8F Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear srs administrator,

I found a problem of making links between databanks with wgetz from srs5.1.0
The error message from the web (error.log) is :
[Mon Feb  2 11:04:14 1998] access to /env/infobiogen/pack/srs5/www/bin/wgetz failed for lovelace.infobiogen.fr, reason: Premature end of script headers

We work on Sun Solaris 2.5 Sparc SUNW,Ultra-Enterprise 4000

Need help

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
---------------------------------------------------
  --------------43F9D54019A253BDEE0C8C8F-- From owner-srs@net.bio.net Sun Feb 01 22:00:00 1998 Path: biosci!daresbury!uninett.no!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: links in srs5 Date: 2 Feb 1998 11:06:26 GMT Organization: EMBL Heidelberg Lines: 19 Distribution: world Message-ID: <6b49bi$cvh@lion.embl-heidelberg.de> References: <34D59E3F.B48EA28D@infobiogen.fr> 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) X-URL: news:34D59E3F.B48EA28D@infobiogen.fr Hello Try running wgetz on the command line. Like wgetz '[swissprot-id:acha_human] > embl' and check what you get. That should help you to identify the real problem! Ramu -- _______________________________________________________________ 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 Mon Feb 02 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!sunqbc.risq.qc.ca!newsxfer.itd.umich.edu!uunet!in1.uu.net!netnews.sbphrd.com!not-for-mail From: Ray Wang Newsgroups: bionet.software.srs Subject: blast and fasta Date: Tue, 03 Feb 1998 14:40:04 -0500 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 11 Message-ID: <34D77294.61E7@mh.us.sbphrd.com> NNTP-Posting-Host: phu824.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) CC: etzold@ebi.ac.uk Could anyone tell me that what version of blast and fasta driver programs are used in SRS5.1? I couldn't make them work in SRS5.1 like I did in SRS5.0.5. In SRS5.0.5, the blast version I used was "BLASTP 1.4.9MP [26-March-1996]" and the fasta version I used was "version 3.0t75 December, 1996. " Does anybody have an idea to make them work? Ray From owner-srs@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.direct.ca!Supernews60!supernews.com!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: SRS 5.1 BUG? Core dump with getz Date: Tue, 10 Feb 1998 14:25:17 +0000 Organization: SEQNET Lines: 32 Distribution: bionet Message-ID: <34E0634D.44CCE775@dl.ac.uk> References: <887118339.2044985357@dejanews.com> 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 4.04 [en] (X11; I; IRIX 5.3 IP12) luca.toldo@merck.de wrote: > > Dear Bionet SRS mainainters, I mailed this question on the 13.01 but so > far got no feedback and the error is perfectly reproducible. I would > appreciate if anybody could provide with feedback. > > I was just wondering if you also are observing on IRIX 6.4 that SRS 5.1.0 > getz produces a core dump when invoked with the following statement: > > getz '[swissprot-id:100k_RAT]' -vf cit > > The same command is not failing when operating on version 5.0.5 > > The swissprot indexes are fully working and operational otherwhise as > could be checked by the wgetz properly working ... > > any feedback is welcome ! > Just to say that on the systems on which we have srs installed (irix5.3 and OSF1) the -vf option of getz does not seem to work with any database. -- ------------------------------------------------------------------- | 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.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Mon Feb 09 22:00:00 1998 From: luca.toldo@merck.de To: etzold@ebi.ac.uk Subject: SRS 5.1 BUG? Core dump with getz Date: Tue, 10 Feb 1998 07:51:18 -0600 Message-ID: <887118339.2044985357@dejanews.com> Newsgroups: bionet.software.srs Organization: Deja News Posting Service Path: biosci!agate!logbridge.uoregon.edu!nntp2.dejanews.com!grunt.dejanews.com!not-for-mail X-Article-Creation-Date: Tue Feb 10 13:45:39 1998 GMT X-Authenticated-Sender: luca.toldo@merck.de X-Http-User-Agent: Mozilla/4.04 [en] (WinNT; I) via proxy gateway CERN-HTTPD/3.0 libwww/2.17 X-Originating-IP-Addr: 155.250.128.1 (wingate.merck.de) Lines: 21 Dear Bionet SRS mainainters, I mailed this question on the 13.01 but so far got no feedback and the error is perfectly reproducible. I would appreciate if anybody could provide with feedback. I was just wondering if you also are observing on IRIX 6.4 that SRS 5.1.0 getz produces a core dump when invoked with the following statement: getz '[swissprot-id:100k_RAT]' -vf cit The same command is not failing when operating on version 5.0.5 The swissprot indexes are fully working and operational otherwhise as could be checked by the wgetz properly working ... any feedback is welcome ! regards Dr. Luca Ida Giovanni TOLDO (Ph.D.) -------------------==== Posted via Deja News ====----------------------- http://www.dejanews.com/ Search, Read, Post to Usenet From owner-srs@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.internetmci.com!192.87.106.104!surfnet.nl!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: Where is the 450000 ? Date: 10 Feb 1998 14:39:42 GMT Organization: Belgian EMBnet Node Lines: 12 Message-ID: <6bpore$5tr$1@mach.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] Dear SRS experts, When I select a protein from the SwissProt and I try to link to HSSP I get an limitexceeded ! Maximum number of "links in buffer" is 450000 error I searched in the Icarus files and in the SRS source code to find where the 450000 limit is defined so that I might adapt it, but I could not find it. Can someone explain me how to proceed ? Guy Bottu From owner-srs@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!uunet!in1.uu.net!netnews.sbphrd.com!not-for-mail From: Ray Wang Newsgroups: bionet.software.srs Subject: Re: blast and fasta Date: Tue, 10 Feb 1998 16:21:09 -0500 Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 15 Message-ID: <34E0C4C5.1979@mh.us.sbphrd.com> References: <34D77294.61E7@mh.us.sbphrd.com> NNTP-Posting-Host: phu824.sbphrd.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (X11; I; SunOS 5.5.1 sun4u) Ray Wang wrote: > > Could anyone tell me that what version of blast and fasta driver > programs are used in SRS5.1? I couldn't make them work in SRS5.1 like I > did in SRS5.0.5. > > In SRS5.0.5, the blast version I used was "BLASTP 1.4.9MP > [26-March-1996]" and the fasta version I used was "version 3.0t75 > December, 1996. " > > Does anybody have an idea to make them work? I have modified the blastdb, it seems that blast works fine now for me. Ray From owner-srs@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!news-han1.dfn.de!news.tu-bs.de!rzlimes.gbf-braunschweig.de!not-for-mail From: "Thomas Heinemeyer" Newsgroups: bionet.software.srs Subject: TRANSFAC 3.3-Announcement Date: 10 Feb 1998 15:25:24 GMT Organization: Gesellschaft fuer Biotechnologische Forschung mbH Lines: 49 Message-ID: <01bd3637$a65ee520$db030101@cyber_tom> NNTP-Posting-Host: gen219.gbf-braunschweig.de X-Newsreader: Microsoft Internet News 4.70.1161 The TRANSFAC server now has made accessible the new release 3.3 of the TRANSFAC database (Heinemeyer et al., 1998, Nucleic Acids Res. 26:364-370): http://transfac.gbf.de/ TRANSFAC is a database on eukaryotic transcription factors and their binding sites. As new features, it visualizes the items of the feature list (FACTOR table) as well as element positions within regulatory regions (GENE table). Moreover, the data volume has increased comprising now 2285 FACTOR and 4602 SITE entries. A new extended search option is available. The SRS 5.1.0 version on the TRANSFAC server also offers access to the databases TRRD (Transcription Regulatory Region Database, Institute of Cytology and Genetics [ICG], Novosibirsk, Russia; N. A. Kolchanov/A. Kel et al.) and to COMPEL, a database on composite elements (joint effort by ICG and GBF). Available at: http://transfac.gbf.de/srs5/ As many users know, the sequence information contained in the SITE table is used by PatSearch 1.1 to interactively scan DNA sequences for potential TF binding sites. This program is accessible at: http://transfac.gbf.de/cgi-bin/patSearch/patsearch.pl An updated library of matrices for transcription factor binding sites is provided which can be used for sequence analysis with MatInspector release 2.1 (Quandt et al., 1995, Nucleic Acids Res. 23:4878-4884). This tool is available at http://transfac.gbf.de/cgi-bin/matSearch/matsearch.pl or at http://www.gsf.de/BIODV/matinspector.html (Thomas Werner and coworkers). Please, forward this mail to your colleagues which may be interested in using these tools. On behalf of the TRANSFAC team: Edgar Wingender Thomas Heinemeyer GBF - Braunschweig, February 10, 1998 ------------------------------------------------------------ TRANSFAC-Team Tel.: +49(0)531 6181 427 Ges. f. Biotechn. Forsch. mbH Fax: +49(0)531 6181 266 Abt. Genomanalyse E-Mail: transfac@gbf.de Mascheroder Weg 1 http://transfac.gbf.de/ D-38124 Braunschweig From owner-srs@net.bio.net Mon Feb 09 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.starnet.net!sdd.hp.com!usc!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: Where is the 450000 ? Date: 10 Feb 1998 15:26:46 GMT Organization: EMBL Heidelberg Lines: 18 Distribution: world Message-ID: <6bprjm$2nn@lion.embl-heidelberg.de> References: <6bpore$5tr$1@mach.vub.ac.be> 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) X-URL: news:6bpore$5tr$1@mach.vub.ac.be Hello grep "links in buffer" *.c link.c: _ErrExit3 (f__limitexceeded, "links in buffer", LNKxBUFFSIZ/8); regards Ramu -- _______________________________________________________________ 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 Tue Feb 10 22:00:00 1998 Path: biosci!AMC.UVA.NL!a.h.vankampen From: a.h.vankampen@AMC.UVA.NL ("A.H. van kampen ", automat) Newsgroups: bionet.software.srs Subject: How to save results of query? Date: 11 Feb 1998 07:35:38 -0800 Organization: Academic Medical Centre Amsterdam Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <34E1C442.CEC95749@amc.uva.nl> NNTP-Posting-Host: net.bio.net Hello, I have another simple question: Is it possible to save all hits from a query IN A SINGLE OPERATION as full entries (including the sequence), in such a format that GCG can deal with it (so seperate files for each entry, or msf files, or something that gcg can import). I know i can select multiple entries and save them in GCG format as full entries, but this gives a single file which can not be read by GCG. Regards, -- --------------------------------------- | Dr. Antoine H.C. van Kampen | | Academic Medical Center Amsterdam | | ADB/ICT-Services | Cluster Research Support | | Meibergdreef 9 | | 1105 AZ Amsterdam, the Netherlands | -------------------------------------------------| | Phone: ++31-20-5667096 | | Fax: ++31-20-5669020 | | Email: a.h.vankampen@amc.uva.nl | | www: http://www.amc.uva.nl/ | ------------------------------------- From owner-srs@net.bio.net Tue Feb 10 22:00:00 1998 Path: biosci!daresbury!uninett.no!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: Re: SRS 5.1 BUG? Core dump with getz Date: Wed, 11 Feb 1998 17:48:12 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 31 Message-ID: <6bso9a$amg$1@niobium.hgmp.mrc.ac.uk> References: <887118339.2044985357@dejanews.com> NNTP-Posting-Host: idefix.ebi.ac.uk X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 luca.toldo@merck.de wrote in message <887118339.2044985357@dejanews.com>... >getz produces a core dump when invoked with the following statement: > >getz '[swissprot-id:100k_RAT]' -vf cit > found the bug. easy to fix: edit getz.c. in function BuildView replace the line ViewAddRootLib (view, LibObjByName ("library", libName)); by ViewAddRootLib (view, libName); recompile getz with srsmake getz cheers thure From owner-srs@net.bio.net Tue Feb 10 22:00:00 1998 Path: biosci!agate!howland.erols.net!europa.clark.net!206.246.194.8!newsxfer.visi.net!rill.news.pipex.net!pipex!server1.netnews.ja.net!hgmp.mrc.ac.uk!not-for-mail From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: Re: How to save results of query? Date: Wed, 11 Feb 1998 17:40:15 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 24 Message-ID: <6bsnqd$ak0$1@niobium.hgmp.mrc.ac.uk> References: <34E1C442.CEC95749@amc.uva.nl> NNTP-Posting-Host: idefix.ebi.ac.uk X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 "A.H. van kampen ", automat wrote in message <34E1C442.CEC95749@amc.uva.nl>... >Hello, > >I have another simple question: > >Is it possible to save all hits from a query IN A SINGLE OPERATION >as full entries (including the sequence), in such a format that GCG can >deal with it (so seperate files for each entry, or msf files, or >something that >gcg can import). > >I know i can select multiple entries and save them in GCG format as >full entries, but this gives a single file which can not be read by GCG. i would save the set in pir format and then use GCG's frompir to convert into single sequence files. before you click on the save button send the chunksize to something large to make sure that only one save operation is necessary thure From owner-srs@net.bio.net Wed Feb 11 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: How to save results of query? Date: 12 Feb 1998 10:58:55 GMT Organization: EMBL Heidelberg Lines: 20 Distribution: world Message-ID: <6buklf$78d@lion.embl-heidelberg.de> References: <34E1C442.CEC95749@amc.uva.nl> <6bui5g$78d@lion.embl-heidelberg.de> 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) X-URL: news:6bui5g$78d@lion.embl-heidelberg.de Hi Sorry, I forgot to mention one more option in the 'download query' page Before pressing save button in 'download query' page also select ' Use View' as Complete Entries Ramu _______________________________________________________________ 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 Feb 11 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: How to save results of query? Date: 12 Feb 1998 10:16:16 GMT Organization: EMBL Heidelberg Lines: 41 Distribution: world Message-ID: <6bui5g$78d@lion.embl-heidelberg.de> References: <34E1C442.CEC95749@amc.uva.nl> 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: a.h.vankampen@amc.uva.nl X-URL: news:34E1C442.CEC95749@amc.uva.nl Hello Yes it is possible! You can do it from the 'Query Manager' page. Go to Query manager page after doing your query Select the query you want to save, press save button. Now you are in the 'Download query page'. Select the chunksize Select the sequence format (select swiss or embl format) select 'use mimetype' as binary ( binary ? do not worry about that) press save button (the browser should offer you now to enter a filename to save) (IF you have local SRS then you can do all the above with 'getz' ! That is the easiest way) In GCG you can use fromembl program to convert all the sequences to gcg format and carry on from there! fromembl writes each entry into separate file. (fromembl works for protein seqeuences as well!) (Note selecting sequence format from SRS does not work with gcg 9.1) If you have trouble let me know. Hope this helps! Ramu -- _______________________________________________________________ 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 Feb 11 22:00:00 1998 Path: biosci!PFIZER.COM!deandp From: deandp@PFIZER.COM ("David P. Dean") Newsgroups: bionet.software.srs Subject: perl SRS.pm? Date: 12 Feb 1998 08:14:42 -0800 Organization: Pfizer Central Research Lines: 9 Sender: daemon@net.bio.net Distribution: world Message-ID: <34E320C0.7B99@pfizer.com> NNTP-Posting-Host: net.bio.net We've just built a local SRS site - and are very glad we did... Does anyone have a PERL5 module available that links in the C API routines? -- David P. Dean (deandp@pfizer.com) Department of Molecular Sciences Pfizer Inc Groton, CT 06340 From owner-srs@net.bio.net Wed Feb 11 22:00:00 1998 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!logbridge.uoregon.edu!pln-w!extra.newsguy.com!lotsanews.com!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: "Thure Etzold" Newsgroups: bionet.software.srs Subject: Re: perl SRS.pm? Date: Thu, 12 Feb 1998 18:54:36 -0000 Organization: MRC Human Genome Mapping Project Resource Centre Lines: 25 Message-ID: <6bvght$msq$1@niobium.hgmp.mrc.ac.uk> References: <34E320C0.7B99@pfizer.com> NNTP-Posting-Host: idefix.ebi.ac.uk X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 "David P. Dean" wrote in message <34E320C0.7B99@pfizer.com>... >We've just built a local SRS site - and are very glad we did... > >Does anyone have a PERL5 module available that links in the C API >routines? Not to my knowledge! There has been a lot of talk about that and i went even so far as creating a simple prototype with the help of a perl expert at Argonne Ntl. lab. It is really easy and the C api seems very suitable for that sort of thing. We don't unfortunately have enough resources to it properly ...any volunteers??? We would pay you a free lunch at the Red Lion in Hinxton! regards Thure From owner-srs@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.14!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: srs5.1 : bug(?) Date: 13 Feb 1998 10:33:01 GMT Organization: EMBL Heidelberg Lines: 20 Distribution: world Message-ID: <6c17gt$rco@lion.embl-heidelberg.de> 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) X-URL: news:bionet.software.srs In srs5.1 (OSF) I get the following message when I try srscheck ++++++> must rebuild index "Comment" for TFCLASS, is not up to date e__allocfail, insufficient memory - error during malloc could not allocate "id-index-object" Ramu _______________________________________________________________ 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 Thu Feb 12 22:00:00 1998 Path: biosci!agate!howland.erols.net!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!hgmp.mrc.ac.uk!not-for-mail From: Peter Rice Newsgroups: bionet.software.srs Subject: Re: srs5.1 : bug(?) Date: 13 Feb 1998 10:47:42 +0000 Organization: The Sanger Centre Lines: 27 Sender: pmr@unst.sanger.ac.uk Message-ID: References: <6c17gt$rco@lion.embl-heidelberg.de> NNTP-Posting-Host: unst.sanger.ac.uk X-Newsreader: Gnus v5.5/Emacs 20.2 Ramu Chenna writes: > In srs5.1 (OSF) > > I get the following message when I try srscheck > > ++++++> must rebuild index "Comment" for TFCLASS, is not up to date > e__allocfail, insufficient memory - error during malloc > could not allocate "id-index-object" The latest Transfac 3.3 release includes updated Icarus files. The original versions had some minor problems, but I have updated them and GBF probably now provide the corrected ones. If not, you can pick up the Sanger versions from http://www.sanger.ac.uk/srs5/ These are fine for me, also on OSF. ... though the only change in tfclass.i or tfclass.is that could affect you is an increased maxNameLen to 20 in tfclass.i -- ---------------------------------------------------------------------- Peter Rice | Informatics Division, The Sanger Centre, E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus, Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/ From owner-srs@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!news-han1.dfn.de!news.tu-bs.de!rzlimes.gbf-braunschweig.de!not-for-mail From: "Thomas Heinemeyer" Newsgroups: bionet.software.srs Subject: TRANSFAC database 3.3 Date: 13 Feb 1998 07:31:51 GMT Organization: Gesellschaft fuer Biotechnologische Forschung mbH Lines: 49 Message-ID: <01bd3850$f4709540$db030101@cyber_tom> NNTP-Posting-Host: gen219.gbf-braunschweig.de X-Newsreader: Microsoft Internet News 4.70.1161 The TRANSFAC server now has made accessible the new release 3.3 of the TRANSFAC database (Heinemeyer et al., 1998, Nucleic Acids Res. 26:364-370): http://transfac.gbf.de/ TRANSFAC is a database on eukaryotic transcription factors and their binding sites. As new features, it visualizes the items of the feature list (FACTOR table) as well as element positions within regulatory regions (GENE table). Moreover, the data volume has increased comprising now 2285 FACTOR and 4602 SITE entries. A new extended search option is available. The SRS 5.1.0 version on the TRANSFAC server also offers access to the databases TRRD (Transcription Regulatory Region Database, Institute of Cytology and Genetics [ICG], Novosibirsk, Russia; N. A. Kolchanov/A. Kel et al.) and to COMPEL, a database on composite elements (joint effort by ICG and GBF). Available at: http://transfac.gbf.de/srs5/ As many users know, the sequence information contained in the SITE table is used by PatSearch 1.1 to interactively scan DNA sequences for potential TF binding sites. This program is accessible at: http://transfac.gbf.de/cgi-bin/patSearch/patsearch.pl An updated library of matrices for transcription factor binding sites is provided which can be used for sequence analysis with MatInspector release 2.1 (Quandt et al., 1995, Nucleic Acids Res. 23:4878-4884). This tool is available at http://transfac.gbf.de/cgi-bin/matSearch/matsearch.pl or at http://www.gsf.de/BIODV/matinspector.html (Thomas Werner and coworkers). Please, forward this mail to your colleagues which may be interested in using these tools. On behalf of the TRANSFAC team: Edgar Wingender Thomas Heinemeyer GBF - Braunschweig, February 10, 1998 ------------------------------------------------------------ TRANSFAC-Team Tel.: +49(0)531 6181 427 Ges. f. Biotechn. Forsch. mbH Fax: +49(0)531 6181 266 Abt. Genomanalyse E-Mail: transfac@gbf.de Mascheroder Weg 1 http://transfac.gbf.de/ D-38124 Braunschweig From owner-srs@net.bio.net Thu Feb 12 22:00:00 1998 Path: biosci!agate!newsgate.duke.edu!news.ysu.edu!Cabal.CESspool!bofh.vszbr.cz!fu-berlin.de!news-ber1.dfn.de!news-ham1.dfn.de!news-han1.dfn.de!news.tu-bs.de!rzlimes.gbf-braunschweig.de!not-for-mail From: "Thomas Heinemeyer" Newsgroups: bionet.software.srs Subject: TRANSFAC 3.3 SRS parsers Date: 13 Feb 1998 16:43:58 GMT Organization: Gesellschaft fuer Biotechnologische Forschung mbH Lines: 17 Message-ID: <01bd389e$37ae4d00$db030101@cyber_tom> NNTP-Posting-Host: gen219.gbf-braunschweig.de X-Newsreader: Microsoft Internet News 4.70.1161 The SRS 5.1.x parsers for TRANSFAC 3.3 are available! Please download at ... http://transfac.gbf.de/cgi-bin/download/download.pl the file named: tf33_i.tar.Z Dr. Thomas Heinemeyer Tel.: ++49(0)531 6181 295 Ges. f. Biotechn. Forsch. mbH Fax: ++49(0)531 6181 266 Abt. Genomanalyse E-Mail: thh@gbf.de Mascheroder Weg 1 http://transfac.gbf.de/Staff/thh.html D-38124 Braunschweig From owner-srs@net.bio.net Tue Feb 17 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-pen-14.sprintlink.net!206.229.87.26!news-east.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!Sprint!newsfeed.direct.ca!Supernews60!supernews.com!uunet!in3.uu.net!munnari.OZ.AU!news.unimelb.edu.au!wehi.edu.au!wehi!janice From: janice@wehi.edu.au (Janice Coventry, Walter and Eliza Hall Institute) Newsgroups: bionet.software.srs Subject: Javascript error message Date: 18 Feb 98 14:30:14 +1000 Organization: Walter & Eliza Hall Institute Lines: 19 Message-ID: <1998Feb18.143014@wehi> NNTP-Posting-Host: wehiu.wehi.edu.au X-Trace: wehid.wehi.EDU.AU 887772787 28466 (None) 128.250.252.27 X-Complaints-To: newsmaster@wehi.edu.au Hi I have noticed that at srs.ebi.ac.uk that if someone has javascript disabled and they are using Netscape4 that a message: SRS requires a javascript enabled browser appears when they try to access the top page. However when I do the same thing I get a blank page. Is there a fix to wgetz that allows us to display this message. Thank you in anticipation Janice ================================================================================ Janice Coventry The Walter and Eliza Hall Institute of Medical Research, P.O. Royal Melbourne Hospital, Victoria, 3050, Australia. Phone: International +61-3-9345-2564 FAX: International +61-3-9347-0852 National 03-9345-2564 National 03-9347-0852 Email: janice@wehi.edu.au =============================================================================== From owner-srs@net.bio.net Wed Feb 18 22:00:00 1998 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!194.162.162.196!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: Re: Javascript error message Date: 19 Feb 1998 10:43:09 GMT Organization: EMBL Heidelberg Lines: 19 Distribution: world Message-ID: <6ch2bt$3qe@lion.embl-heidelberg.de> References: <1998Feb18.143014@wehi> 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) X-URL: news:1998Feb18.143014@wehi Hello I think you should include the following in your srswww.i toppage section. Ramu _______________________________________________________________ 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 Feb 18 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.software.srs Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 19 Feb 1998 02:00:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199802191000.CAA09704@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 Mon Feb 23 22:00:00 1998 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: jtsr-stock@jtsr-stock.com Newsgroups: bionet.software.srs Subject: HOT STOCK(JTSR)-Double Your Money By Easter!! Date: 24 Feb 1998 11:05:39 -0000 Lines: 26 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <6cu9i3$58c@mserv1.dl.ac.uk> Original-To: Friend@dl.ac.uk You have been carefully selected to receive the following as a person obviously interested in this subject based upon your previous internet postings, or visits to one of our affiliate web sites. If you have received this message in error, please accept our apology as a responsible e-mailer, and reply with the word REMOVE in the subject line. You will be automatically excluded from future e-mailings. Thank you for your consideration and help in making the Internet spam-free. ***** Visit http://www.jtsr-stock.com or call 888-295-6365 For Complete Information. **** NEWS FLASH **** 2/20/98 Analysts correct - JT's Stock price up 40% in last week!! Who said opportunity only knocks once. JT's Restaurant is about to be one of the fastest growing Restaurant chains. Under valued stock situations presently $3.00 per share. Analysts predict stock to go as high as $5.00 by Easter and could go up to $10.00 by end of 1998. Stock symbol JTSR on NASDAQ. If you had invested just $100.00 in 1955 in Mcdonalds, it would be worth over $100 million today. $1000 would be worth over $1 billion. Here is another opportunity for you. Visit us at http://www.jtsr-stock.com or call 1-888-295-6365. The contents of this message have been provided for the review of potential investors only and does not constitute an offering of securities. From owner-srs@net.bio.net Wed Feb 25 22:00:00 1998 Path: biosci!agate!howland.erols.net!newsfeed.internetmci.com!195.99.66.215!news-feed1.eu.concert.net!newsfeed.skynet.be!news.belnet.be!news.vub.ac.be!ben!gbottu From: gbottu@ben.vub.ac.be (Guy Bottu) Newsgroups: bionet.software.srs Subject: A nasty bug in the SRS link indexing Date: 26 Feb 1998 15:17:03 MET X-Date: 18 Feb 1998 12:11:35 GMT Organization: Belgian EMBnet Node Lines: 20 Message-ID: <6cej5n$b72$1@mach.vub.ac.be> NNTP-Posting-Host: ben.vub.ac.be X-Newsreader: TIN [version 1.2 PL2] Dear SRS developers and fellow SRS server managers, While trying to implement a direct link between PIR and EMBL/GENBANK I ran into trouble. After some searching I found that the cause was a bug in the SRS software itself. It seems that when there is e.g. an Icarus line : $link:[@SWISSPROT_DB to:@?EMBL_DB token:'link|EMBL' toField:@DF_Accession] not just tokens with code EMBL are put in the index, but all tokens. To convince yourself of this, try the following : search in SWISSPROT the entry with ID HA12_MOUSE then make the link to EMBL you will see that besides the two correct EMBL entries you also find A02201 which is not related to the sequence SWISSPROT:HA12_MOUSE but happens to have the same accession number as the corresponding PIR entry. SRS is great, but keeping it alive costs a lot of sweat and tears... Guy Bottu From owner-srs@net.bio.net Thu Feb 26 22:00:00 1998 Path: biosci!organon.oss.akzonobel.nl!j.rullmann From: j.rullmann@organon.oss.akzonobel.nl ("J.A.C. Rullmann", Ton) Newsgroups: bionet.software.srs Subject: problems building Genbank (GCG) Date: 27 Feb 1998 00:12:10 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 35 Sender: daemon@net.bio.net Distribution: world Message-ID: <34F67501.B173C5DF@organon.oss.akzonobel.nl> NNTP-Posting-Host: net.bio.net As a newcomer to SRS I ran into problems building the indices for GenBank (GCG format). I'm using SRS 5.1.0 on IRIX 6.4. The GenBank release is 104 (12/97), as obtained from GCG. I tried to modify genbank.i to switch from EMBL to GCG format. srsbuild -info genbank seems to work fine. srsbuild -w genbank gives the following: > ...processing GENBANK > ...processing /u04/gcggenbank/gb_ba.ref > ...processing /u04/gcggenbank/gb_ba.seq > Entry name mismatch: ref=A16SRRNA, seq= > But I can't see anything wrong with the file headers: > % head /u04/gcggenbank/gb_ba.ref > >>>>A16SRRNA 7/97 > X87617 Actinomycete (genus unknown) 16S ribosomal RNA. 7/97 > > .... > > % head /u04/gcggenbank/gb_ba.seq > >>>>A16SRRNA 7/97 2BIT Len: 1497 > X87617 Actinomycete (genus unknown) 16S ribosomal RNA. 7/97 > This problem did not occur when building the SwissProt indices. Any suggestions? Thanks! Ton Rullmann MDI-RIM group, Organon, the Netherlands From owner-srs@net.bio.net Thu Feb 26 22:00:00 1998 Path: biosci!daresbury!usenet From: Martin Hilbers Newsgroups: bionet.software.srs Subject: Re: problems building Genbank (GCG) Date: Fri, 27 Feb 1998 09:52:10 +0000 Organization: SEQNET Lines: 46 Distribution: bionet Message-ID: <34F68CCA.2B1073B9@dl.ac.uk> References: <34F67501.B173C5DF@organon.oss.akzonobel.nl> 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 4.04 [en] (X11; I; IRIX 5.3 IP12) To: j.rullmann@organon.oss.akzonobel.nl J.A.C. Rullmann, Ton wrote: > > As a newcomer to SRS I ran into problems building the indices for > GenBank (GCG format). > I'm using SRS 5.1.0 on IRIX 6.4. The GenBank release is 104 (12/97), as > obtained from GCG. > > I tried to modify genbank.i to switch from EMBL to GCG format. > srsbuild -info genbank seems to work fine. > srsbuild -w genbank gives the following: > > > ...processing GENBANK > > ...processing /u04/gcggenbank/gb_ba.ref > > ...processing /u04/gcggenbank/gb_ba.seq > > Entry name mismatch: ref=A16SRRNA, seq= > > > I've seen this also and the fix was changing the line ('ORIGIN' {$Not} lnT {$App})+ lnT)? to ('ORIGIN' {$Not} lnT {$App})+ lnT lnT?)? in the entry production in genbank.is. Check http://www.seqnet.dl.ac.uk/srs5bin/cgi-bin/wgetz?-fun+PageIcarusFile+-l+GENBANK+-ifile+is for a genbank.is which works with gcg genbank. It also handles the citation field, and does the hyperlinks in the db_xref fields in the feature tables correctly. Cheers, Martin PS - release 104 ??? - the latest release is 105 ! -- ------------------------------------------------------------------- | 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.seqnet.dl.ac.uk/ | ------------------------------------------------------------------- From owner-srs@net.bio.net Thu Feb 26 22:00:00 1998 Path: biosci!AMC.UVA.NL!a.h.vankampen From: a.h.vankampen@AMC.UVA.NL ("A.H. van kampen ", automat) Newsgroups: bionet.software.srs Subject: strings in view? Date: 27 Feb 1998 04:43:25 -0800 Organization: Academic Medical Centre Amsterdam Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <34F6B48C.3922DEF3@amc.uva.nl> NNTP-Posting-Host: net.bio.net Hello, Is it possible to define views in views.i that not only include fields but also text strings. I'm using srs 5.0.5 Regards, -- --------------------------------------- | Dr. Antoine H.C. van Kampen | | Academic Medical Center Amsterdam | | ADB/ICT-Services | Cluster Research Support | | Meibergdreef 9 | | 1105 AZ Amsterdam, the Netherlands | -------------------------------------------------| | Phone: ++31-20-5667096 | | Fax: ++31-20-5669020 | | Email: a.h.vankampen@amc.uva.nl | | www: http://www.amc.uva.nl/ | ------------------------------------- From owner-srs@net.bio.net Thu Feb 26 22:00:00 1998 Path: biosci!newshost.lanl.gov!awabi.library.ucla.edu!208.134.241.18!newsfeed.internetmci.com!194.162.162.196!newsfeed.nacamar.de!news-kar1.dfn.de!news.embl-heidelberg.de!usenet From: Ramu Chenna Newsgroups: bionet.software.srs Subject: srscheck problems Date: 27 Feb 1998 14:08:41 GMT Organization: EMBL Heidelberg Lines: 50 Distribution: world Message-ID: <6d6hd9$ksk@lion.embl-heidelberg.de> 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) X-URL: news:bionet.software.srs?ALL Hi Problem: 1 ========== embl.i icarus file (at EMBL) has three databases namely emblnew, embl, emblest defined! when i try srscheck -l emblest it is fine since EMBLEST is updated! But when i say srscheck -l 'emblnew emblest' then it says ======> must build indices for library "EMBLNEW" but in the srsupdate file it has lines to update EMBLEST also! This problem is there with srs5_05 and srs5_1 ======== Problem No:2 with SRS5.1 while building indices I get SRSDB:embl.is:87: error: insufficient memory - error during malloc, could not allocate "Cursor object" Any insight ? Ramu _______________________________________________________________ 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 ______