From owner-gdb@net.bio.net Wed Jun 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!news.tamu.edu!128.194.15.2!leland From: leland@straylight.tamu.edu (Leland Ellis) Newsgroups: bionet.molbio.gdb Subject: DolPhinS and Human Cytogenetic Maps Followup-To: bionet.molbio.gdb Date: 09 Jun 1994 21:48:24 GMT Organization: W.M. Keck Center for Genome Informatics, Institute of Biosciences and Technology, Texas A&M University, Houston Lines: 54 Distribution: world Message-ID: NNTP-Posting-Host: straylight.tamu.edu Human Cytogenetic Maps For use with our new Display PostScript client, DolPhinS, we now have a complete set of Human Cytogenetic Maps in the Keck-IBT (.ki) file format. In the directory for each chromosome will be found three .ki files: human.#.cyto.Exact.ki human.#.cyto.Overlap.ki human.#.cyto.Inclusive.ki Upon loading one of the chromosome files into DolPhinS, clicking on a cytogenetic band (or the band name) launchs an Exact, Overlap or Inclusive query, respectively, to the Genome Database (GDB) WWW Server at Johns Hopkins. Results are returned in HTML in a Mosaic window. For further info, see these URLs: Keck-IBT: http://keck.tamu.edu/ibt.html DolPhinS: http://keck.tamu.edu/cgi/DolPhinS/DolPhinS.html AGsKI and the .ki file format: http://keck.tamu.edu/cgi/demo/AGsKI/agski.html human cytomaps: http://keck.tamu.edu/cgi/demo/AGsKI/human/ email: leland@straylight.tamu.edu -- ******************************************************************** Leland Ellis, Ph.D. Professor of Biochemistry and Biophysics Director, W.M. Keck Center for Genome Informatics Institute of Biosciences and Technology Texas A&M University 2121 Holcombe Houston, Texas 77030 ******************************************************************** email: leland@straylight.tamu.edu URL: http://straylight.tamu.edu/straylight.html GenomeMOO: telnet://straylight.tamu.edu:7777/ MOOmail: Wizard in GenomeMOO ******************************************************************** "We all live in the world as we imagine it, as we create it." Andrey Tarkovsky, 'Sculpting in Time -- Reflections on the Cinema' ******************************************************************** From owner-gdb@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!trane.uninett.no!nntp.uio.no!NewsWatcher!user From: olam@radium.uio.no (Ola Myklebost) Newsgroups: bionet.molbio.gdb Subject: Re: DolPhinS and Human Cytogenetic Maps Followup-To: bionet.molbio.gdb Date: Mon, 13 Jun 1994 12:47:36 +0100 Organization: Inst for Cancer Research, Oslo Lines: 23 Distribution: world Message-ID: References: NNTP-Posting-Host: pcdnr05.uio.no Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit In article , leland@straylight.tamu.edu (Leland Ellis) wrote: > > Human Cytogenetic Maps > > For use with our new Display PostScript client, DolPhinS, we now have a > complete set of Human Cytogenetic Maps in the Keck-IBT (.ki) file format. > Upon loading one of the chromosome files into DolPhinS, clicking > on a cytogenetic band (or the band name) launchs an Exact, > Overlap or Inclusive query, respectively, to the Genome Database > (GDB) WWW Server at Johns Hopkins. Results are returned in > HTML in a Mosaic window. Sounds great! Is this available for the mac also? -- Ola Myklebost Email ola.myklebost@labmed.uio.no Dept of Tumor Biology Inst for Cancer Research Tel +47-2293-4299 The Norwegian Radium Hospital Fax +47-2252-2421 N-0310 OSLO, Norway From owner-gdb@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!newsfeed.pitt.edu!dsinc!netnews.upenn.edu!duong From: duong@chestnut.chem.upenn.edu (Duc Duong) Newsgroups: bionet.molbio.proteins,bionet.molbio.gdb Subject: how to calculate H coordinates of NH bond with pdb file Date: 13 Jun 1994 16:11:51 GMT Organization: NMR Biochemistry Graduate Research Lab Lines: 9 Message-ID: <2ti0g7$pmu@netnews.upenn.edu> NNTP-Posting-Host: chestnut.chem.upenn.edu Xref: biosci bionet.molbio.proteins:2075 bionet.molbio.gdb:204 hi.. I tried to calculate the Hydrogen coordinates of the N-H bond in the pdb file (no need for the side chain Hydrogen, or OH).. I looked thru Quanta4.0 and it does it nicely thru CHARM Energy.. so Is there an algorithm available out there?? This one seems very useful so anyone has any reference or suggestion?? Thank you. dduc From owner-gdb@net.bio.net Sun Jun 12 23:00:00 1994 Path: biosci!CHPC.UTEXAS.EDU!mwitten From: mwitten@CHPC.UTEXAS.EDU Newsgroups: bionet.molbio.gdb Subject: URGENT QUESTION Date: 13 Jun 1994 10:15:37 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 39 Sender: daemon@net.bio.net Distribution: world Message-ID: <9406131716.AA17890@morpheus> NNTP-Posting-Host: net.bio.net Question: I am interested in any help from anyone out there on the following subject. We have become an information gathering society. One of the areas of interest is the gathering of large databases of information. I was wondering if anyone out there might know of databases of biomedical information and how to access them. For example, GenBank, census data, databases of medical images, databases of population statistics, environmental toxicity data, dental data, etc. If you know of such data, would you please send me the following information: Name of Database: Is the database public or private: How to contact database or database owner. I will summarize the responses for the list. This is a rather urgent request so, rapid answers would be appreciated. Do not worry about duplicating others. Feel free to cross post this note to any other lists that might be appropriate. Thanks, Matthew Witten, Ph.D. Head, Department of Applications Research and Development Associate Director UT System Center For High Performance Computing Balcones Research Center, 1.154 CMS 10100 Burnet Road, Austin, TX 78758-4497 USA Phone: (512) 471-2472 FAX: (512) 471-2445 E-MAIL MWITTEN@CHPC.UTEXAS.EDU From owner-gdb@net.bio.net Mon Jun 13 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.molbio.gdb Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 14 Jun 1994 02:00:12 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 319 Sender: daemon@net.bio.net Distribution: world Message-ID: <199406140900.CAA21492@net.bio.net> NNTP-Posting-Host: net.bio.net Four important items follow: How to cancel e-mail subscriptions to BIOSCI newsgroups, BIOSCI archive searching, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our BIOSCI user directory, please take a few minutes to complete and return the form below. If your personal information has changed since you listed yourself, please send us a complete new updated form. We can not make manual revisions to existing entries. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net **** How to cancel a BIOSCI e-mail subscription **** If you want to cancel your e-mail subscription to this group, PLEASE DO NOT POST YOUR UNSUBSCRIBE REQUEST TO THE NEWSGROUP ADDRESS (NOR REPLY TO A MESSAGE POSTED TO THE NEWSGROUP)!!! This would send your request to all of the readers of the newsgroup, but it might still not be seen by the BIOSCI staff - thus you would annoy many people and possibly not accomplish your goal anyway. 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If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.). Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form. Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET MAKING SURE THAT YOUR INFORMATION IS CURRENT This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form --------------------------------- If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form. or Rob Harper's gopher site in Europe as follows: > Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. 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Thanks again for your cooperation! --------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment: From owner-gdb@net.bio.net Tue Jun 14 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!cs.utexas.edu!news.tamu.edu!128.194.15.2!leland From: leland@straylight.tamu.edu (Leland Ellis) Newsgroups: bionet.molbio.gdb Subject: Re: DolPhinS and Human Cytogenetic Maps Followup-To: bionet.molbio.gdb Date: 15 Jun 1994 12:05:02 GMT Organization: W.M. Keck Center for Genome Informatics, Institute of Biosciences and Technology, Texas A&M University, Houston Lines: 40 Distribution: world Message-ID: References: NNTP-Posting-Host: straylight.tamu.edu In-reply-to: olam@radium.uio.no's message of Mon, 13 Jun 1994 12:47:36 +0100 Hello, no, DolPhinS was developed in a Unix environment using X11/Motif for the windowing architecture and Display PostScript (DPS) for rendering of information. It is likely, based on user responses thusfar, that DolPhinS will be ported to other Unix environments, and most Unix X servers will have the DPS extensions (several do now). We plan to release the source code in the not too distant future, as soon as we have incorporated user suggestions and a few additional enhancements to D's functionality. If there are Mac developers that would like to look at what is involved in such a port, we would be very supportive in spirit, and keep them up-to-date about where D's functionality is heading in the future. Cheers, L. -- ******************************************************************** Leland Ellis, Ph.D. Professor of Biochemistry and Biophysics Director, W.M. Keck Center for Genome Informatics Institute of Biosciences and Technology Texas A&M University 2121 Holcombe Houston, Texas 77030 ******************************************************************** email: leland@straylight.tamu.edu URL: http://straylight.tamu.edu/straylight.html GenomeMOO: telnet://straylight.tamu.edu:7777/ MOOmail: Wizard in GenomeMOO ******************************************************************** "We all live in the world as we imagine it, as we create it." Andrey Tarkovsky, 'Sculpting in Time -- Reflections on the Cinema' ******************************************************************** From owner-gdb@net.bio.net Mon Jun 20 23:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!agate!howland.reston.ans.net!pipex!uknet!liv!ma92ajb From: ma92ajb@liverpool.ac.uk (Mr A.J.S. Burn) Subject: Sequence Dbases for peptides Message-ID: Sender: news@liverpool.ac.uk (News System) Nntp-Posting-Host: uxd.liv.ac.uk Organization: The University of Liverpool X-Newsreader: TIN [version 1.2 PL2] Date: Tue, 21 Jun 1994 13:17:04 GMT Lines: 1 From owner-gdb@net.bio.net Mon Jun 20 23:00:00 1994 Path: biosci!rutgers!gatech!nntp.msstate.edu!emory!europa.eng.gtefsd.com!news.umbc.edu!haven.umd.edu!umd5.umd.edu!ram From: ram@mbisgi.umd.edu (Ram Samudrala) Newsgroups: bionet.molbio.evolution,sci.bio,bionet.molbio.gdb Subject: Relationships between genes... Message-ID: <2u74pd$bpr@umd5.umd.edu> Date: 21 Jun 94 16:33:49 GMT Organization: The Centre for Advanced Research in Biotechnology Lines: 17 NNTP-Posting-Host: indigo3.carb.nist.gov X-Newsreader: TIN [version 1.2 PL0] Xref: biosci bionet.molbio.evolution:1802 sci.bio:9724 bionet.molbio.gdb:209 I am looking for information pertaining to the relationship between various genes in a chromosome for the various chromosomes that have been sequenced. In particular, I am looking for genes which are believed to have arisen out of gene duplication events. Any pointers to where such information can be found will be appreciated. I searched a bit through the WWW but couldn't come up with anything remotely close. Thanks! --Ram ram@elan1.carb.nist.gov If you didn't care what happened to me, and I didn't care for you, we would zig zag our way through the boredom and pain occasionally glancing up through the rain wondering which of the buggers to blame and watching for pigs on the wing. ---Pink Floyd From owner-gdb@net.bio.net Tue Jun 21 23:00:00 1994 Path: biosci!agate!ames!elroy.jpl.nasa.gov!usc!howland.reston.ans.net!vixen.cso.uiuc.edu!uwm.edu!post.its.mcw.edu!not-for-mail From: ltseng@post.its.mcw.edu (Leon Fu Tseng) Newsgroups: bionet.molbio.gdb Subject: Proenkephalin mRNA Date: 22 Jun 1994 09:20:10 -0500 Organization: Medical College of Wisconsin; Milwaukee Wisconsin Lines: 7 Message-ID: <2u9haq$adk@post.its.mcw.edu> NNTP-Posting-Host: post.its.mcw.edu X-Newsreader: TIN [version 1.2 PL1] I am looking for the structure and sequence for Proenkephalin mRNA. I have not searched the WWW database because I am a novice to the Usenet. Please respond by e-mail. Thanks in advance, Dr. Leon Tseng Medical College of Wisconsin From owner-gdb@net.bio.net Tue Jun 21 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!pipex!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!seb1005 From: seb1005@mole.bio.cam.ac.uk (Steven Brenner) Newsgroups: bionet.molbio.gdb Subject: Re: Mac HTML+forms WWW client? Date: 22 Jun 1994 17:43:47 GMT Organization: University of Cambridge, England Lines: 21 Message-ID: <2u9t8j$59n@lyra.csx.cam.ac.uk> References: <1994Jun22.135533.13409@emba.uvm.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk brianf@med.uvm.edu (Brian Foley) writes: > Is there a Mac WWW client that supports HTML+forms? I currently >have NCSA Mosaic v1.03 and it doesn't seem to support forms. There are two such clients, but both are currently alpha test versions, and apparently contain significant bugs. They are : NCSA Mosaic for Macintosh: ftp://ftp.ncsa.uiuc.edu/Mosaic/Mac/NCSAMosaicMac.200A1.sit.hqx and EINET MacWeb ftp://ftp.einet.net/einet/mac/macweb/macweb0.98alpha.sea.hqx -- Steven E. Brenner | S.E.Brenner@bioc.cam.ac.uk MRC Laboratory of Molecular Biology | Office: +44 223 402221 Hills Road | Fax: +44 223 213556 Cambridge CB2 2QH, UK | Lab: +44 223 333660 From owner-gdb@net.bio.net Tue Jun 21 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!vixen.cso.uiuc.edu!uiuc!cjamison From: cjamison@news.cso.uiuc.edu (Curt Jamison) Newsgroups: bionet.molbio.evolution,sci.bio,bionet.molbio.gdb Subject: Re: Relationships between genes... Date: 22 Jun 1994 15:14:29 GMT Organization: Community Systems Laboratory, University of Illinois, Urbana-Champaign Lines: 26 Distribution: world Message-ID: <2u9kgl$rre@vixen.cso.uiuc.edu> References: <2u74pd$bpr@umd5.umd.edu> NNTP-Posting-Host: badger.ncsa.uiuc.edu Xref: biosci bionet.molbio.evolution:1804 sci.bio:9743 bionet.molbio.gdb:212 In article <2u74pd$bpr@umd5.umd.edu>, ram@mbisgi.umd.edu (Ram Samudrala) writes: |> I am looking for information pertaining to the relationship between |> various genes in a chromosome for the various chromosomes that have |> been sequenced. In particular, I am looking for genes which are |> believed to have arisen out of gene duplication events. |> |> Any pointers to where such information can be found will be |> appreciated. I searched a bit through the WWW but couldn't come up |> with anything remotely close. |> |> Thanks! |> |> --Ram You don't mention which organism you're interested in. If any organism will do, you might try ACeDB, which contains the genetic map, physical map, and sequences for C. elegans. There is a searchable index available via gopher and Mosaic, but the best way to work with it is to have it local (assuming you have a Sun or a PC running Linux). -- Curt Jamison cjamison@csl.ncsa.uiuc.edu These opinions are entirely my own and bear no relation to those of my employers and/or reality From owner-gdb@net.bio.net Tue Jun 21 23:00:00 1994 Newsgroups: bionet.molbio.gdb Path: biosci!agate!howland.reston.ans.net!pipex!doc.ic.ac.uk!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!uunet!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brian Foley) Subject: Mac HTML+forms WWW client? Message-ID: <1994Jun22.135533.13409@emba.uvm.edu> Sender: news@emba.uvm.edu Organization: University of Vermont -- Division of EMBA Computer Facility X-Newsreader: TIN [version 1.2 PL1] Date: Wed, 22 Jun 1994 13:55:33 GMT Lines: 9 Is there a Mac WWW client that supports HTML+forms? I currently have NCSA Mosaic v1.03 and it doesn't seem to support forms. -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * ******************************************************************** From owner-gdb@net.bio.net Thu Jun 23 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!news-feed-1.peachnet.edu!insosf1.infonet.net!usenet.ee.pdx.edu!fastrac.llnl.gov!sundance.llnl.gov!osi-east2.es.net!pnl-oracle!netnews.nwnet.net!mule.fhcrc.org!fred!schen From: schen@fred (Shu-Chih Chen) Newsgroups: bionet.molbio.gdb Subject: about inducible promoter Date: 24 Jun 1994 01:51:05 GMT Organization: Fred Hutchinson Cancer Research Center Lines: 13 Message-ID: <2ude69$tn0@mule.fhcrc.org> NNTP-Posting-Host: fred.fhcrc.org X-Newsreader: TIN [version 1.2 PL2] : Hi: Could someone help me to find a review on the inducible promoter? Best of all, if we could obtain a vector with the inducible promoter. Thank you for your assistance. Shu-Chih Chen