From owner-embldatabank@net.bio.net Mon May 01 23:00:00 1995 Path: biosci!daresbury!trane.uninett.no!nac.no!Norway.EU.net!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!newsrelay.iastate.edu!bvc.edu!yuqian From: yuqian@bvc.edu (Suicidal Freshman) Newsgroups: bionet.molbio.bio-matrix,bionet.molbio.embldatabank Subject: New Dedicated Bio-tech/science/chem BBS Message-ID: <1995May2.124050.10897@bvc.edu> Date: 2 May 95 12:40:50 CDT Organization: Buena Vista College, Storm Lake, IA Lines: 27 Xref: biosci bionet.molbio.bio-matrix:578 bionet.molbio.embldatabank:495 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% A NEW BBS IS ONLINE AND NEEDS PEOPLE LIKE YOU TO HELP IT PROSPER The IDT Online Information System is now up and running and needs intelligent users such as yourselves. Anyone interested in Chemistry or Biology or any twist of the two is more than welcome. If you are a user of Oligonucleotides, there is an online order system that allows you to place your order directly into the production facility for 48 hour turnaround. THERE IS ABSOLUTELY NO CHARGE FOR USAGE. YOU DO NOT HAVE TO BE A CUSTOMER TO USE THE SYSTEM Just a sample of some of the discussion forums: Parsitology Classifieds Employment Chemical Engineering Computer Software Biochemistry Programming Molecular Medicine Genetics Organic Chemistry Oligo Design Scientific Humor BioPhysics Cell Biology Internet Topics Biomed Engineering Late Breaking News Immunology NeuroScience Suggestions The system is in place, and we are looking for good users, and a few Forum Moderators, so: Check it out: telnet 204.71.106.202 or telnet idtdna.com %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From owner-embldatabank@net.bio.net Fri May 05 23:00:00 1995 Path: biosci!WEIZMANN.WEIZMANN.AC.IL!CSMLN From: CSMLN@WEIZMANN.WEIZMANN.AC.IL ("m.lakshmi narayanan") Newsgroups: bionet.molbio.embldatabank Subject: crystallography position (fwd) (fwd) Date: 6 May 1995 01:09:19 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: <950506.110606.+0300.CSMLN@WEIZMANN.WEIZMANN.AC.IL> NNTP-Posting-Host: net.bio.net Dear Sir/Madam, I am a chemist(M.Sc.)- cum - crystallographer(Ph.d.) Looking for a suitable position in a research laboratory. Those who have positions available may please ask for cv/biodata. Research Interest: 1. Crystallography (Macromolecular/Small molecular) 2. drug designing 3. molecular modelling 4. Protein, DNA structure analysis expecting an earlier response thanking you sincerely yours M. Lakshmi Narayanan Department of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL From owner-embldatabank@net.bio.net Tue May 09 23:00:00 1995 Path: biosci!rutgers!uwm.edu!spool.mu.edu!usenet.eel.ufl.edu!europa.chnt.gtegsc.com!news.sprintlink.net!EU.net!news2.EUnet.fr!ceph.cephb.fr!szobo From: szobo@ceph.cephb.fr (Geraldine Szoboszlai) Newsgroups: bionet.molbio.embldatabank,bionet.molbio.genbank,bionet.molbio.gdb,bionet.genome.chromosomes Subject: Oncogenes database Date: 10 May 1995 10:47:37 +0200 Organization: Fondation J. Dausset - CEPH Lines: 6 Distribution: world Message-ID: <3opuj9$4aa@ceph.cephb.fr> NNTP-Posting-Host: ceph.cephb.fr Keywords: oncogene Xref: biosci bionet.molbio.embldatabank:497 bionet.molbio.genbank:2020 bionet.molbio.gdb:325 bionet.genome.chromosomes:579 I m looking for a database of cytogenetic localisation of known oncogenes and antioncogenes. Can anybody help me ? Please reply by mail, thank you. From owner-embldatabank@net.bio.net Thu May 11 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!bshomer From: bshomer@ebi.ac.uk (Benny Shomer) Subject: EMBL WWW Nucleotide Sequence Submission System Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Fri, 12 May 1995 15:02:51 GMT Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 72 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% EMBL WWW Nucleotide Sequence Submission System %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Dear Colleague, The EMBL Nucleotide Sequence Database at the European Bioinformatics Institute (EBI) announces a World Wide Web (WWW) submission tool which provides a fast and convenient way to submit nucleotide sequence data and associated biological information to the database. The system is compatible with every known WWW browser (e.g. Mosaic, Netscape, Macweb, Lynx) on all the common platforms (i.e. X-windows, PC's and Macintosh). You may access the WWW submission tool through the EBI WWW server at: http://www.ebi.ac.uk/ under the heading "EMBL Nucleotide Sequence Database", or use the direct URL: http://www.ebi.ac.uk/subs/emblsubs.html When using the system for the first time, you are kindly requested to read the general help document provided through the first page of the submission tool. After connecting to the EBI WWW server, a sequence of forms will enable you to prepare your data submission as efficiently and easily as possible. During any stage of submission, you may find a context sensitive help by selecting the help button provided. EBI staff will process your submission within 24-48 hours of receipt and then by e-mail communicate to you the database accession number(s) assigned to your data. Database entries created by the new WWW submission tool and submitted to the EMBL Nucleotide Sequence Database at the EBI will be exchanged and shared among the International Collaboration of Nucleotide Sequence Databases (DDBJ, EMBL, GenBank) and it is therefore only necessary to submit to one database. For further information, please contact: datalib@ebi.ac.uk Yours sincerely, Benny Shomer. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Benny Shomer External Biological Liasion Officer, EMBL outstation - The EBI, Hinxton Hall, Hinxton,Cambridge CB10 1RQ, UK Tel: +44-223-494437 Fax: +44-223-494468 Email: bshomer@EBI.ac.uk http://www.ebi.ac.uk/ebi_docs/staff/benny.html ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-embldatabank@net.bio.net Tue May 16 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!agate!hpg30a.csc.cuhk.hk!hkuxb.hku.hk!hkuxa.hku.hk!billyli From: billyli@hkuxa.hku.hk (Billy Li) Subject: Number of bases? Message-ID: Sender: usenet@hkuxb.hku.hk (USENET News System) Nntp-Posting-Host: hkuxa.hku.hk Organization: The University of Hong Kong X-Newsreader: TIN [version 1.1 PL6] Date: Wed, 17 May 1995 01:55:34 GMT Lines: 12 I do not use EMBL but does anyone know how many bases are in EMBL at present? Thanks in advance. -- Billy Li, email: billyli@hkuxa.hku.hk Assistant Lecturer, Department of Statistics, University of Hong Kong. Tel: (852) 28591987 Fax: (852) 28589041 From owner-embldatabank@net.bio.net Tue May 16 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!gatech!swrinde!howland.reston.ans.net!pipex!oleane!jussieu.fr!univ-lyon1.fr!news From: duret@acnuc.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.molbio.embldatabank Subject: Re: Number of bases? Date: 17 May 1995 06:30:24 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 21 Distribution: world Message-ID: <3pc560$src@cismsun.univ-lyon1.fr> References: Reply-To: duret@acnuc.univ-lyon1.fr NNTP-Posting-Host: acnuc.univ-lyon1.fr In article CDx@hkuxb.hku.hk, billyli@hkuxa.hku.hk (Billy Li) writes: > >I do not use EMBL but does anyone know how many bases are in EMBL >at present? > In EMBL Library Release 42 (March 1995), there was 309,892 sequences, for 265,066,849 bases. Regards, ================================================================ Laurent Duret duret@biomserv.univ-lyon1.fr Tel: +33 72.44.81.42 Fax: +33 78.89.27.19 Laboratoire de Biometrie, Genetique et Biologie des Populations Bat 741 - URA CNRS 243 Universite Claude Bernard - Lyon I 43, Bd du 11 Novembre 1918 69622 Villeurbanne cedex FRANCE ================================================================ From owner-embldatabank@net.bio.net Tue May 16 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: Number of bases? Message-ID: <1995May17.095335.14906@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: Date: Wed, 17 May 1995 09:53:35 GMT Lines: 20 Billy Li (billyli@hkuxa.hku.hk) wrote: : I do not use EMBL but does anyone know how many bases are in EMBL : at present? As the poster is from a 'department of statistics', it is important to know that the plain number of bases is fairly insignificant, as lots of duplicates, fragments and overlapping sequences exist. The actual number of entries has been 300000, and the current update file is another 100000 approximately. This is good to guess learning the accuracy of the precise figure - the current growth will outpace any printed article in days. Regards Reinhard Doelz -- R.Doelz Klingelbergstr.70| Tel. x41 61 267 2247 Fax x41 61 267 2078| Biocomputing CH 4056 Basel| electronic Mail doelz@ubaclu.unibas.ch| Biozentrum der Universitaet Basel|-------------- Switzerland ---------------| EMBnet Switzerland:info@ch.embnet.org From owner-embldatabank@net.bio.net Thu May 18 23:00:00 1995 Newsgroups: bionet.software.gcg,bionet.molbio.embldatabank,bionet.software Path: biosci!bloom-beacon.mit.edu!usc!cs.utexas.edu!howland.reston.ans.net!EU.net!sun4nl!sci.kun.nl!caos.kun.nl!jackl From: jackl@caos.kun.nl (Jack Leunissen) Subject: EMBL to NBRF/GCG conversion, rel 2.2 Message-ID: <1995May19.082810.9355@caos.kun.nl> Keywords: sequence conversion, GCG, EMBL, NBRF/PIR Sender: root@caos.kun.nl (System PRIVILEGED Account) Nntp-Posting-Host: cammsg1.caos.kun.nl Organization: CAOS/CAMM Date: Fri, 19 May 1995 08:28:10 GMT Lines: 37 Xref: biosci bionet.software.gcg:1178 bionet.molbio.embldatabank:502 bionet.software:12110 Dear Collegues, Release 2.2 of the program "EMBL2NBRF" is available. It converts EMBL flat files into PIR/NBRF format, which can be used by most sequence analysis programs, or packages like GCG. New in the current release is the ability to perform "on the fly" splitting of data files into the EMBL taxonomic division files. This is increasingly important, considering the size of esp. the EST section in the EMBL updates: on May 15th, the EST section alone carried over 100,000 entries, of a total of 120,000 in the cumulative updates! Here is an example for the README file: % zcat cumulative.dat.Z | emb2nbrf -m -n emnew -s emnew.info -x -- which reads the (decompressed) data from standard input ("--"), splitting the entries in the EMBL cumulative updates into their taxonomic division files (-x), and naming them "emnew_ba", "emnew_est", etc. The progress of the action is monitored (-m), and the summary is written to a file (-s). A small C-shell script is also provided to create the GCG header files. The program can be obtained by anonymous ftp to "ftp.caos.kun.nl", in the directory "/pub/molbio/embl2nbrf". The URL = ftp://ftp/caos.kun.nl/pub/molbio/embl2nbrf/ Or send an e-mail to Jack Leunissen (jackl@caos.kun.nl). Regards, Jack -- Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center, Univ. of Nijmegen Email: jackl@caos.kun.nl | Toernooiveld Tel. : +31 80 65 22 48 | 6525 ED Nijmegen, The Netherlands Fax : +31 80 65 29 77 | URL=http://www.caos.kun.nl/ From owner-embldatabank@net.bio.net Mon May 22 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!ix.netcom.com!netnews From: nngo@ix.netcom.com Newsgroups: bionet.molbio.embldatabank Subject: testing Date: Tue, 23 May 1995 17:11:30 GMT Organization: Netcom Lines: 1 Distribution: world Message-ID: <3pt50m$qib@ixnews3.ix.netcom.com> NNTP-Posting-Host: ix-sj9-10.ix.netcom.com This is only a test. Please ignore. From owner-embldatabank@net.bio.net Wed May 24 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!uchinews!woodlawn!ddw2 From: ddw2@woodlawn.uchicago.edu (David Wang) Subject: ## Problem Retrieving EMBL-BITNET ... HELPP! ## X-Nntp-Posting-Host: midway.uchicago.edu Message-ID: Sender: news@midway.uchicago.edu (News Administrator) Reply-To: ddw2@midway.uchicago.edu Organization: University of Chicago -- Academic Information Technologies Date: Thu, 25 May 1995 21:27:19 GMT Lines: 22 Hello, My name is David Wang and recently a postdoc in our lab has had problems retrieving sequence(s) off EMBL. The address it gives to retrieve the sequence is: NETSERV@EMBL:BITNET The wierd thing is that it gives one accession number: DS6748 that contains 67-sequences! That's bizarre if you ask me. Anyways, any help you could render would be most appreciated. My email address is listed below; please email me as I rarely read this newsgroup. Thank you so much. David Wang ddw2@midway.uchicago.edu From owner-embldatabank@net.bio.net Fri May 26 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!bloom-beacon.mit.edu!gatech!news.sprintlink.net!demon!uknet!warwick!news.dcs.warwick.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!stoehr From: stoehr@ebi.ac.uk (Peter Stoehr) Subject: Re: ## Problem Retrieving EMBL-BITNET ... HELPP! ## Sender: news@ebi.ac.uk (Mr news) Message-ID: <1995May26.135221@ebi.ac.uk> Date: Fri, 26 May 1995 12:52:21 GMT Lines: 29 References: Organization: European BioInformatics Institute In article , ddw2@woodlawn.uchicago.edu (David Wang) writes: > Hello, > > My name is David Wang and recently a postdoc in our lab has had problems > retrieving sequence(s) off EMBL. The address it gives to retrieve the > sequence is: > > NETSERV@EMBL:BITNET > > The wierd thing is that it gives one accession number: > > DS6748 > > that contains 67-sequences! That's bizarre if you ask me. David, The address is NETSERV@EBI.AC.UK (the bitnet address was phased out some years ago). This was a supplied as a sequence alignment rather than an original sequence submission. DS6748 is not a nucleotide databadse accession number. You can get it from our anonymous FTP server ftp.ebi.ac.uk in the file pub/databases/embl/align/ds6748.dat or by e-mail to Netserv@ebi.ac.uk with the command: GET ALIGN:DS6748.DAT Regards, Peter Stoehr EMBL - EBI From owner-embldatabank@net.bio.net Wed May 31 23:00:00 1995 Path: biosci!bcm!cs.utexas.edu!swrinde!emory!sol.ctr.columbia.edu!news.mindlink.net!vanbc.wimsey.com!scipio.cyberstore.ca!news.Direct.CA!usenet From: Akio Abe Newsgroups: bionet.molbio.embldatabank Subject: DNA sequence of pGFP Date: 1 Jun 1995 08:41:41 GMT Organization: Internet Portal Services Lines: 12 Message-ID: <3qjug5$3st@stud.Direct.CA> NNTP-Posting-Host: d230.portal.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; 68K) X-URL: news:bionet.molbio.embldatabank Dear Sir; I am looking for a sequence data of plasmid pGFP, encoding green fluorescence gene. Please let me know the FTP site of sequence data or any information. I am look forward to hearing soon from you. AKIO ABE University of British Columbia akioabe@portal.ca From owner-embldatabank@net.bio.net Wed May 31 23:00:00 1995 Path: biosci!biosci!not-for-mail From: stoehr@ebi.ac.uk (Peter Stoehr) Newsgroups: bionet.molbio.embldatabank,embnet.general,bionet.announce Subject: Notice of Accession Number format change Date: 1 Jun 1995 10:09:41 -0700 Organization: European BioInformatics Institute Lines: 34 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: <1995Jun1.132303@ebi.ac.uk> Xref: biosci bionet.molbio.embldatabank:509 bionet.announce:2151 Notice of Accession Number format change Nucleotide Sequence Database Collaborative Agreement 31 May 1995 Currently, accession numbers used by the nucleotide sequence databases consist of one prefix letter followed by 5 digits. EST projects and projects to add patent data have accelerated the need to extend the accession number space. It is projected that the databases will run out of accession numbers within 8 to 10 months. It is clear that: * As much notice as possible should be given to users and software developers * The change should make a large enough space that another change will not be necessary in the foreseeable future. * The accession number should continue to be readily identifiable as a DDBJ/EMBL/GenBank accession number. The collaborators concluded that: * A new form of accession number will be created, defined as an 8-character alphanumeric string, beginning with two upper case letters and followed only by digits (e.g., SR004562). Leading and trailing zeros are significant. The letter 'O' will not be used. * Existing 6-character accession numbers will remain as they are, and will never be transformed to an 8-character form. * New accession numbers will not be used before February 1, 1996. The groups agree to avoid using new accession numbers as long as possible after that. The International Nucleotide Sequence Databases DDBJ/EMBL/GenBank