From owner-chromosomes@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!howland.reston.ans.net!ux1.cso.uiuc.edu!uwm.edu!linac!uchinews!raistlin!timbuk.cray.com!walter.cray.com!calamity!mwd From: mwd@cray.com (Mark Dalton) Newsgroups: bionet.genome.chromosomes Subject: Re: discs large gene - Drosophila Summary: large discs Keywords: Drosophila Message-ID: <1993Jun3.020019.15999@walter.cray.com> Date: 3 Jun 93 07:00:19 GMT Followup-To: mwd@carina.cray.com Organization: Cray Research, Inc. Lines: 50 Originator: mwd@calamity Nntp-Posting-Host: calamity.cray.com Written by: 09p2@bioch.ox.ac.uk I am looking for information on this gene - anyone out there have a recent reference on either its location and/or sequence. Failing that does anyone know what the exact spelling is? I can't seem to pick the damn thing up in Med-line!! Perhaps it is to recent... Many thanks... Geoff --------------------< End of message >------------------------------------ This is accessable through gopher: In gopher: Get to other sites (all in world) IUbio FlyBase (Or whereever else Flybase maybe) Redbook search Redbook with: 'discs' bunch of stuff deleted: 24. discs absent, small, or homeotic: see dash. --> 25. discs large: see dlg1. --> 26. dlg1: discs large. # dlg1: discs large location: 1-34.82. synonym: l(1)10Bf. references: Stewart, Murphy, and Fristrom, 1972, Dev. Biol. 27: 71-83. Gateff, 1978, Biol. Rev. 53: 123-68. 1978, Science 200: 1448-59. Kiss, Szabad, and Major, 1978, Mol. Gen. Genet. 164: 77-83. Perrimon, 1988, Dev. Biol. 127: 392-407. Woods and Bryant, 1989, Dev. Biol. 134: 222-35. There is a lot more information available. If you have questions on using gopher let me know. I have more information on how to use gopher and where to get it. It is posted on a lot of the Bionet groups. Thanks! Mark -- Mark Dalton Cray Research, Inc. Eagan, MN 55121 Internet: mwd@cray.com From owner-chromosomes@net.bio.net Wed Jun 02 23:00:00 1993 Path: biosci!mrc-crc.ac.uk From: smercer@mrc-crc.ac.uk (Mr. S.J. Mercer) Newsgroups: sci.bio.technology,sci.med,bionet.announce,bionet.general,bionet.genome.chromosomes,bionet.sci-resources Subject: The Chromosome Abnormality Database Keywords: Chromosome Database Gene Mapping Syndrome Message-ID: <1993Jun3.143619.21453@crc.ac.uk> Date: 3 Jun 93 14:36:19 GMT Sender: kristoff@net.bio.net Followup-To: poster Organization: MRC Human Genome Resource Centre Lines: 30 Approved: bionews-moderator@net.bio.net Xref: biosci sci.bio.technology:355 sci.med:15949 bionet.announce:567 bionet.general:5063 bionet.genome.chromosomes:26 bionet.sci-resources:748 Nntp-Posting-Host: tin THE CHROMOSOME ABNORMALITY DATABASE The Chromosome Abnormality Database (CAD) is a centralised repository of records of human chromosome abnormalities, and is available for researchers to search free of charge. Established in early 1991, the CAD now contains nearly forty thousand records of acquired and constitutional chromosome abnormalities contributed by over forty cytogenetics laboratories throughout the United Kingdom. Although there is a considerable bias towards recent cases, the data stretch back over twenty years and include information on the availability of cell lines and other stored material. Searches of the database may be performed free of charge by contacting the database manager, Dr Mercer at the address below, or directly by the researcher through the computing facilities maintained by the UK Human Genome Mapping Program. Dr S. Mercer, The Chromosome Abnormality Database, Oxford Medical Genetics Laboratory, Churchill Hospital, Headington, OXFORD OX3 7LJ ENGLAND Tel: +44 865 226003 Fax: +44 865 226006 Email: simon@bioch.ox.ac.uk From owner-chromosomes@net.bio.net Thu Jun 03 23:00:00 1993 Path: biosci!daresbury!mrccrc!gwilliam From: gwilliam@crc.ac.uk (Gary Williams x3294) Newsgroups: bionet.genome.chromosomes Subject: Re: The Chromosome Abnormality Database Keywords: Chromosome Database Gene Mapping Syndrome Message-ID: <1993Jun4.083902.2989@crc.ac.uk> Date: 4 Jun 93 08:39:02 GMT References: <1993Jun3.143619.21453@crc.ac.uk> Sender: news@crc.ac.uk Organization: MRC Human Genome Resource Centre Lines: 39 Nntp-Posting-Host: gallium In article <1993Jun3.143619.21453@crc.ac.uk> smercer@mrc-crc.ac.uk (Mr. S.J. Mercer) writes: > > THE CHROMOSOME ABNORMALITY DATABASE > >The Chromosome Abnormality Database (CAD) is a centralised repository of >records of human chromosome abnormalities, and is available for researchers >to search free of charge. > >Searches of the database may be performed free of charge by contacting the >database manager, Dr Mercer at the address below, or directly by the researcher >through the computing facilities maintained by the UK Human Genome Mapping >Program. To register as a user of the UK HGMP-RC facilities, please mail or fax to the following address: Christine Bates The HGMP Resource Centre Clinical Research Centre Watford Road Harrow MIDDX HA1 3UJ Tel: 081-869 3446 Fax: 081-869 3807 Email: C.Bates@uk.ac.crc Registration is open to any bona fide academic, whether based in the UK or elsewhere. Registration is not restricted to those directly involved in human genome mapping. -- GARY WILLIAMS, Computing Services, Janet: G.Williams@UK.AC.CRC MRC Human Genome Mapping Project, Internet: G.Williams@CRC.AC.UK Watford Rd, HARROW, Middx, HA1 3UJ, UK ** Sequence databases have ** Tel 081-869 3294 Fax 081-423 1275 ** about a 3% error content ** From owner-chromosomes@net.bio.net Sat Jun 05 23:00:00 1993 Path: biosci!MINDLINK.BC.CA!Arthur_Ma From: Arthur_Ma@MINDLINK.BC.CA (Arthur Ma) Newsgroups: bionet.genome.chromosomes Subject: F.I.S.H. control groups stats Message-ID: Date: 6 Jun 93 19:15:00 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 37 To all you F.I.S.H. (Fluorescent In-situ Hybridisation) experts out there.... I work in the Cytogenetic Laboratory doing clinical work including F.I.S.H. studies. I am in the process of establishing control groups for Oncor's DXZ1 probe. We are scoring five hundred interphase nuclei in each of the ten female and ten male control groups. Thus we can refer to the statistics of the control groups in our query Turner's and Klinefelter's cases. Our bone marrow section already established their controls for the Oncor Y probe. They used it to track Post BMT(bone marrow transplant) cases. What I want to know, especially from the Biostatisticians, is how I should treat the data. For the female control group (X probe): obviously the majority of the nuclei wil have two signals, but there's always a percentage of single signals (it is important when you have query Turner's cases to interpret whether the percentage of single signal is significant compare to the control group). And vice-versa, I have to establish whether a certain number of duo signals in the male control nuclei is significant. The bone marrow section uses the 95% Confidence limit, specifically the Upper Confidence Limit for the Y probe. Biostats was a long time ago for me so HELP!!!! Thanks for any help you can provide!! -------------------------------------------------------- | Arthur Ma | | Vancover General Hospital | | Cytogenetic Laboratory | | 855 West 12th Avenue | | Vancouver, B.C. | | CANADA V5Z 1M9 | | (604)875-4129 | | | | E-MAIL ADDRESS: ARTHUR_MA@MINDLINK.BC.CA | -------------------------------------------------------- From owner-chromosomes@net.bio.net Wed Jun 09 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.genome.chromosomes Subject: IMPORTANT BIOSCI INFORMATION Message-ID: <9306100900.AA06466@net.bio.net> Date: 10 Jun 93 09:00:02 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 143 Three important items follow: BIOSCI archive searching by e-mail, the BIOSCI FAQ, and the BIOSCI User Address Directory form. If you have not yet listed yourself in our e-mail address directory, please take a few minutes to complete and return the form below. If your address information has changed since you listed yourself, please send us an updated form. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net **** SEARCHING BIOSCI ARCHIVES WITH WAISMAIL **** E-mail users can search the BIOSCI archives by using our waismail e-mail server. For instructions send the message help to waismail@net.bio.net. Leave the Subject: line blank. Other methods of searching the archives via WAIS and gopher are described in the BIOSCI FAQ ... **** BIOSCI FREQUENTLY ASKED QUESTIONS (FAQ) SHEET **** New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. **** BIOSCI USER ADDRESS DIRECTORY **** Please take this opportunity to add you name and address information to the BIOSCI User Address Database if you have not already done so. Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database will serve as a directory that will enable biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. The address database will be indexed for WAIS and waismail access (waismail is our WAIS e-mail server, more below) and will also be available for access via other gopher sites if they wish to permit it. The raw unindexed data will be available for FTP from net.bio.net and is atomized sufficiently to allow import into your local RDBMS should you so desire. 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 our WAIS source or waismail e-mail server from time-to-time to see if your address information is still up-to-date. Send the message help to waismail@net.bio.net for instructions on using waismail. Leave the Subject: line in your message blank. (Note as of 5 May 93 - the address database will be updated nightly and will go on-line soon after we have collected and processed the initial rush of data). IMPORTANT INSTRUCTIONS - PLEASE READ CAREFULLY Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). Please do NOT extend your responses past the end of each line (80 characters) or alter any of the field identifiers such as "first name: ". Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction. On the date: line, please enter the date in the DD-MM-YY format, e.g., 05-05-93 for 5 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 05-05-93, not 5-5-93. Note that the "e-mail network: " line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on. If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form! In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously. 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-chromosomes@net.bio.net Thu Jun 10 23:00:00 1993 Path: biosci!ATGENOME.BIO.UPENN.EDU!cbell From: cbell@ATGENOME.BIO.UPENN.EDU (Callum Bell - Ecker lab) Newsgroups: bionet.genome.chromosomes Subject: STR nomenclature Message-ID: <9306111851.AA08275@atgenome.bio.upenn.edu> Date: 11 Jun 93 18:51:52 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 13 Can some one provide me with a reference that gives conventions for naming simple tandem repeats? For example (gaa)n is also (aga)n and (tct)n, etc. Are there conventions for all possible STRs? ---------------------------------------------------------------------- Callum Bell | cbell@atgenome.bio.upenn.edu Department of Biology | phone (215) 898-0946 University of Pennsylvania | FAX (215) 898-8780 PA 19104-6018 | ---------------------------------------------------------------------- From owner-chromosomes@net.bio.net Fri Jun 11 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!uunet!munnari.oz.au!constellation!aardvark.ucs.uoknor.edu!aardvark.ucs.uoknor.edu!broe From: broe@aardvark.ucs.uoknor.edu (Bruce Roe) Newsgroups: bionet.genome.chromosomes Subject: Who is Mapping Human Chromosome 9? Message-ID: <12JUN199307285110@aardvark.ucs.uoknor.edu> Date: 12 Jun 93 12:28:00 GMT Organization: University of Oklahoma - University Computing Services Lines: 19 Nntp-Posting-Host: loopback.uoknor.edu News-Software: VAX/VMS VNEWS 1.41 Lines: 19 Hi, We have almost completed the sequence of the ca. 275kb human cAbl gene on chromosome 9 but sadly two of the cosmid clones representing about 60kb in two regions of intron1 are not what we thought they were. Before we take up offers from some very kind folks who said they would be glad to screen libraries for us I was wondering if anyone has or knows of anyone with cosmid, P1, etc clones covering the human cAbl gene's first intron? We do have a couple of YACs that may cover this region but if anyone has a cosmid contig on chrom9 covering this region we'd love to hear about it. Thanks in advance........bruce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ Bruce A. Roe Professor of Chemistry and Biochemistry / / Dept. of Chem. and Biochem. INTERNET: BROE@aardvark.ucs.uoknor.edu \ \ University of Oklahoma BITNET: BROE@uokucsvx / / 620 Parrington Oval, Rm 208 AT&TNET: 405-325-4912 or 405-325-7610 \ \ Norman, Oklahoma 73019 FAXnet: 405-325-6111 / - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From owner-chromosomes@net.bio.net Fri Jun 11 23:00:00 1993 Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!cs.utexas.edu!uunet!munnari.oz.au!constellation!aardvark.ucs.uoknor.edu!aardvark.ucs.uoknor.edu!broe From: broe@aardvark.ucs.uoknor.edu (Bruce Roe) Newsgroups: bionet.genome.chromosomes Subject: Anyone cloned the mouse homologs of human cabl and bcr Message-ID: <12JUN199307391139@aardvark.ucs.uoknor.edu> Date: 12 Jun 93 12:39:00 GMT Organization: University of Oklahoma - University Computing Services Lines: 14 Nntp-Posting-Host: loopback.uoknor.edu News-Software: VAX/VMS VNEWS 1.41 Lines: 14 Hi again, Now that we are close to finishing the human cAbl (chrom9) and BCR (chrom22) gene sequences, we'd also like to do some comparative sequence studies with corresponding regions from other organisms. Does anyone know of anyone who may have mapped and obtained cosmids or other clones covering either cAbl or BCR regions from the mouse? Again, thanks in advance........bruce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ Bruce A. Roe Professor of Chemistry and Biochemistry / / Dept. of Chem. and Biochem. INTERNET: BROE@aardvark.ucs.uoknor.edu \ \ University of Oklahoma BITNET: BROE@uokucsvx / / 620 Parrington Oval, Rm 208 AT&TNET: 405-325-4912 or 405-325-7610 \ \ Norman, Oklahoma 73019 FAXnet: 405-325-6111 / - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From owner-chromosomes@net.bio.net Sun Jun 13 23:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!usc!sol.ctr.columbia.edu!news.kei.com!newsstand.cit.cornell.edu!cornell!uw-beaver!netnews.nwnet.net!news.u.washington.edu!news.u.washington.edu!news From: dadler@u.washington.edu (David A. Adler) Newsgroups: bionet.genome.chromosomes Subject: Chromosome Idiograms, human and mouse Message-ID: <1virosINNb3o@news.u.washington.edu> Date: 14 Jun 93 21:49:16 GMT Reply-To: dadler@u.washington.edu Organization: University of Washington Lines: 47 NNTP-Posting-Host: larry.pathology.washington.edu Hello Bionauts, I am pleased to announce the availability via Gopher of computerized idiograms of human and mouse chromosomes. The idiograms are in PostScript (PostScript is a trademark of Adobe Systems Inc.) and were created to allow band-by-band manipulation with certain graphics software, such as Adobe Illustrator, Aldus FreeHand, Corel Draw, Altsys Virtuoso. These files can be freely used by individuals for personal use or by non-profit institutions. (Commercial use is prohibited - contact David Adler for licensing information.) You will find tar.Z and stuffed/binhexed (.sit.hqx) compressed files of the entire human and mouse sets and subdirectories (human and mouse) containing the individual ascii PostScript files. The Gopher site can be found, geographically, under Washington, University of Washington, Pathology Department OR point your Gopher at: larry.pathology.washington.edu, port 70 Feedback is welcome - suggestions, corrections, criticisms, compliments can be emailed to: dadler@u.washington.edu I plan to add scanned images of actual chromosomes for human and mouse in the near future. And would also like to add other species - Drosophila polytenes? (camera obscura and/or scanned micrographs). If you have images that you think would be of interest to others or are looking for particular chromosome images please contact me. Questions can be emailed to me at: dadler@u.washington.edu I would also like to acknowledge support, suggestions, criticisms from Christine Disteche, George Martin and Kris Carroll at the University of Washington and Roland Hubner at the University of Liege, and the University of Washington Department of Pathology for computer facilities. David -- David A. Adler Pathology SM-30 University of Washington Seattle, WA 98195 (206) 543-0716 (phone) (206) 543-3644 (fax) "Science is nothing but trained and organized common sense" T.H.Huxley From owner-chromosomes@net.bio.net Sun Jun 13 23:00:00 1993 Path: biosci!flovax.LANL.GOV!tesmer From: tesmer@flovax.LANL.GOV Newsgroups: bionet.genome.chromosomes Subject: mailing list Message-ID: <9306142232.AA25184@beta.lanl.gov> Date: 14 Jun 93 22:32:24 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 Please drop me from your mailing list. Thanks From owner-chromosomes@net.bio.net Wed Jun 16 23:00:00 1993 Path: biosci!agate!doc.ic.ac.uk!warwick!pipex!uknet!pavo.csi.cam.ac.uk!mrc-lmb.cam.ac.uk!njw From: njw@mrc-lmb.cam.ac.uk (White Nick) Newsgroups: bionet.genome.chromosomes Subject: Re: Chromosome Idiograms, human and mouse Message-ID: <1993Jun17.152411.16026@infodev.cam.ac.uk> Date: 17 Jun 93 15:24:11 GMT References: <1virosINNb3o@news.u.washington.edu> Sender: news@infodev.cam.ac.uk (USENET news) Organization: MRC Laboratory of Molecular Biology, Cambridge UK Lines: 33 Nntp-Posting-Host: al.mrc-lmb.cam.ac.uk In article <1virosINNb3o@news.u.washington.edu> dadler@u.washington.edu writes: >Hello Bionauts, >I am pleased to announce the availability via Gopher of computerized >idiograms of human and mouse chromosomes. The idiograms are in PostScript >(PostScript is a trademark of Adobe Systems Inc.) and were created to >allow band-by-band manipulation with certain graphics software, such as >Adobe Illustrator, Aldus FreeHand, Corel Draw, Altsys Virtuoso. These >files can be freely used by individuals for personal use or by non-profit >institutions. etc...... >David A. Adler Pathology SM-30 >University of Washington Seattle, WA 98195 >(206) 543-0716 (phone) (206) 543-3644 (fax) >"Science is nothing but trained and organized common sense" >T.H.Huxley Sorry to post to the net but I couldn't contact you via e-mail. I'd like a copy of the chromosome 20 pic but unfortunately haven't got a gopher connection. Is it possible to ftp? If yes what's the machine address and where are the files? Many thanks Nick njw@mrc-lmb.cam.ac.uk Nick J. White Haematological Medicine University of Cambridge MRC Centre, Hills Road Cambridge England From owner-chromosomes@net.bio.net Fri Jun 18 23:00:00 1993 Path: biosci!a1.mscf.upenn.edu!fischbeck From: fischbeck@a1.mscf.upenn.edu ("Dr. Kenneth Fischbeck") Newsgroups: bionet.genome.chromosomes Subject: chromosome 22 YACs Message-ID: <85528091603991.21348@MSCF> Date: 19 Jun 93 17:19:01 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 11 As part of the human genome center here in Philadelphia, we have been screening genomic YAC libraries with chromosome 22 STSs. We would like to make the fruits of this labor available to the genome-mapping community at large. Please contact me if you would like a list of chromosome 22 loci with identified YAC clones. K. Fischbeck (fischbeck@a1.mscf.upenn.edu) From owner-chromosomes@net.bio.net Wed Jun 23 23:00:00 1993 Path: biosci!uwm.edu!msuinfo!netnews.upenn.edu!paradigm.dental.upenn.edu!user From: wra@biochem.dental.upenn.edu (Bill Abrams) Newsgroups: bionet.genome.chromosomes Subject: 373A Data Collection V1.2.0 Message-ID: Date: 24 Jun 93 21:18:09 GMT Sender: news@netnews.upenn.edu Followup-To: bionet.genome.chromosomes Organization: University of Pennsylvania Lines: 12 Nntp-Posting-Host: paradigm.dental.upenn.edu In using the latest version of Data Collection software for the ABI373A DNA sequencer (V 1.2.0), we have noted the following problem. The software no longer checks to see if sufficient disk space is available on the hard drive before starting data collection as was the case for earlier versions. When the hard drive drops to approximately 4 MBytes of available disk space, data collection stops, although electrophoresis continues. Older versions of the software used to issue a warning at the initiation of a run, when insufficient disk space was available. If collection stops, interupt run on ABI main unit, go to the finder, discard old files, empty trash, and resume run on ABI unit. Data collection will resume with the next scan. From owner-chromosomes@net.bio.net Thu Jun 24 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!torn!news.ccs.queensu.ca!qucdn!forsdyke From: FORSDYKE@QUCDN.QueensU.CA Newsgroups: bionet.genome.chromosomes Subject: 17th.INT.CONGR.GENETICS:NEW ABSTRACT DEADLINE Message-ID: <93176.094600FORSDYKE@QUCDN.QueensU.CA> Date: 25 Jun 93 13:46:00 GMT Organization: Queen's University at Kingston Lines: 10 17th INTERNAT. CONGRESS GENETICS: NEW ABSTRACTS DEADLINE I have today received the following note from the Secretary General of the 17th INTERNATIONAL CONGRESS OF GENETICS, Prof. Derek Smith: "I have incorporated a note to the effect that late posters can be accepted with an abstract deadline of July 19th in our final advertise ments being dispatched to NATURE and SCIEMCE today" Derek Smith. June 25th 1993 Sincerely, D.R.Forsdyke From owner-chromosomes@net.bio.net Mon Jun 28 23:00:00 1993 Path: biosci!MENDEL.LLNL.GOV!greg From: greg@MENDEL.LLNL.GOV Newsgroups: bionet.genome.chromosomes Subject: Re: What is the Human Genome Project?!?!? Message-ID: <9306291618.AA02305@mendel.llnl.gov.> Date: 29 Jun 93 16:18:32 GMT Sender: daemon@net.bio.net Reply-To: Greg Lennon Distribution: bionet Lines: 12 For a recent overview of the Human Genome Project, see Maynard Olson's paper in the May 15, 1993 PNAS (vol. 90, pp. 4338-4344.) Greg Lennon Human Genome Center, L-452 Lawrence Livermore National Lab Livermore, CA 94550 USA Email: greg@mendel.llnl.gov Phone: (510) 422-5711 Fax: (510) 423-3608 From owner-chromosomes@net.bio.net Mon Jun 28 23:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!wupost!decwrl!decwrl!netcomsv!netcom.com!jordan From: jordan@netcom.com (Jordan A. Bortz) Newsgroups: bionet.genome.chromosomes Subject: What is the Human Genome Project?!?!? Message-ID: Date: 29 Jun 93 06:45:02 GMT Organization: NETCOM On-line Communication Services (408 241-9760 guest) Lines: 22 Excuse me for being an ignoramus but: What the heck is the human genome project? I mean, I've heard a lot about it, and software I wrote is being used on it, but who is funding it, what are it's goals, and what will the results of the research be? I've heard the project is to map every chromosme in the human body. Well, okay. But how will you find out what each chromosome does? Also, I've heard that something like 10% of the human genes have been patented already... IS this true? Can you really patent a gene? Who will own the patents to all the genes discovered by the human genome project? Jordan -- +--------------------------------------------------------------+ | Jordan A.Bortz, Tigre Object Systems, Inc. 408 426 5308 | | jordan@netcom.com | Advanced Development Environments| +--------------------------------------------------------------+ From owner-chromosomes@net.bio.net Mon Jun 28 23:00:00 1993 Path: biosci!WELCHGATE.WELCH.JHU.EDU!rrobbins From: rrobbins@WELCHGATE.WELCH.JHU.EDU (Robert Robbins) Newsgroups: bionet.genome.chromosomes Subject: Re: What is the Human Genome Project?!?!? Message-ID: Date: 29 Jun 93 11:22:27 GMT References: <9306290830.AA13323@net.bio.net> Sender: daemon@net.bio.net Distribution: bionet Lines: 82 On 29 Jun 1993, Jordan A. Bortz wrote: > Excuse me for being an ignoramus but: > > What the heck is the human genome project? > Short answer to a big question: in the US, the research is funded by the National Center for Human Genome Research of the NIH, and by the Health Effects and Life Science Research Division of the Office of Health and Environmental Research of the Department of Energy. As for what the project is trying to accomplish, try the following computer analogy: We now know that information is passed from parent to offspring in genuinely (not metaphorically) digital form. Each parent contributes a 3.3-billion character long string of information, encoded as nucleotide sequences in 23 chromosomes. So, the intructions in, say, a single human sperm cell are equivalent to 3.3 gigabytes of information encoded on some mass storage device. The goal of the human genome project is (1) to obtain an image of that mass stoarge device (i.e., to get the DNA sequence for the chromosomes) and (2) to reverse engineer the 3.3 gigabytes of files all the way back to the design specs (i.e., to understand how these digitally encoded sequences work). For a longer version of this analogy, see: Robbins, R. J., 1992. Database and computational challenges in the human genome project. IEEE Engineering in Medicine and Biology Magazine, 11:25-34. > I've heard the project is to map every chromosme in the human body. > Well, okay. But how will you find out what each chromosome does? How would you go about reverse engineering codes, if all you had were the binaries and if you didn't know the instruction set being used or even the chip on which the codes would run? A fair bit of cleverness is called for, more than can be explained in a quick email response. > Also, I've heard that something like 10% of the human genes have been > patented already... IS this true? Can you really patent a gene? Who > will own the patents to all the genes discovered by the human genome > project? Probably less than 5 % of human genes are even known, much less patented. However, it is possible to patent biological molecules if you have developed ways to turn them into products. For example, suppose heart attacks are brought on, in part, because of the lack of some protein or another. If you can isolate the gene that codes for that protein, you can then make that protein in quantity and sell it as a drug. Pharmaceutical companies have a great interest in patenting genes and other biological molecules, if they can form the basis for developing therapeutical substances. As for who will own the patents, they will belong to whomever (1) develops the technology to produce useful products and (2) files for patent protection. Under the technology transfer act passed during the Reagan administration, primary intellectual property rights in work done with federal support resides with the grantee, not with the government (subject to a variety of restrictions). This was intended to speed the flow of ideas from basic research into the development of products, which is, after all, what makes the economy grow and ultimately provides the tax revennues to support basic research. ====================================================================== Robert J. Robbins Applied Research Laboratory Phone: (410) 955-9637 Johns Hopkins University FAX: (410) 614-0434 2024 E. Monument Street Baltimore, MD 21205 rrobbins@welchgate.welch.jhu.edu ====================================================================== From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!math.ohio-state.edu!darwin.sura.net!news-feed-1.peachnet.edu!umn.edu!csus.edu!netcom.com!kaminski From: kaminski@netcom.com (Peter Kaminski) Newsgroups: bionet.genome.chromosomes,misc.health.alternative,sci.med.telemedicine Subject: Re: Paternity question Message-ID: Date: 1 Jul 93 08:09:42 GMT References: Distribution: usa Organization: The Information Deli - via Netcom / San Jose, California Lines: 24 Supersedes: Xref: biosci bionet.genome.chromosomes:45 misc.health.alternative:4137 sci.med.telemedicine:387 In greene@neyman.ucdavis.edu (Mary Greene) writes: >How many days from conception to birth? Is it 260? 38 weeks (= 266 days) from conception to birth, 40 if you're talking to a doctor (since they count from first day of last period, which is roughly two weeks prior to actual conception). Note that this is the peak of a bell curve; "normal" deliveries can occur up to two weeks before or after the due date. >>If a man has A- blood, what are the blood types his offspring >>could have (not knowing the mother's blood type)? >Depending on the mother, his offspring could be A, AB, or O, all + or -. >>To be POSITIVE of who the father of a child is, what would be the >>next kinds of identification after the blood type? >"Molecular genetic fingerprinting" (from, say a blood sample) can exclude >almost all non-fathers. >Usual disclaimers apply; I'm not a medical professional. >Pete From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!math.ohio-state.edu!howland.reston.ans.net!agate!news.ucdavis.edu!neyman.ucdavis.edu!greene From: greene@neyman.ucdavis.edu (Mary Greene) Newsgroups: bionet.genome.chromosomes,misc.health.alternative,sci.med.telemedicine Subject: Paternity question Message-ID: Date: 1 Jul 93 02:28:17 GMT Sender: usenet@ucdavis.edu (News Administrator) Distribution: usa Organization: University of California, Davis Lines: 10 Xref: biosci bionet.genome.chromosomes:44 misc.health.alternative:4136 sci.med.telemedicine:386 Originator: greene@neyman.ucdavis.edu How many days from conception to birth? Is it 260? If a man has A- blood, what are the blood types his offspring could have (not knowing the mother's blood type)? To be POSITIVE of who the father of a child is, what would be the next kinds of identification after the blood type? -- From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!fcircus.sat.tx.us!Jason_Burrell From: Jason_Burrell@fcircus.sat.tx.us (Jason Burrell) Newsgroups: bionet.genome.chromosomes Subject: Re: What is the Human Genome Project?!?!? Message-ID: <9307010620.AA01dc5@fcircus.sat.tx.us> Date: 1 Jul 93 06:20:34 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 37 In <9306290830.AA13323@net.bio.net>, jordan@netcom.com (Jordan A. Bortz) writes: > Excuse me for being an ignoramus but: > > What the heck is the human genome project? > ...[Rest of message deleted to conserve bandwidth]... > +--------------------------------------------------------------+ > I would also like to know this. I am not a scientist, but a high-school student who has been lucky enough to obtain a USENET account. I've been reading this bionet group for a long time, but have posted exactly twice (counting this time) :-) Genetics is one of my many hobbies.... How can someone patent a gene? If this runs like everything else, I'll be owned by some biological research corperation :-) Last but not least, (I am being a REAL ignoramus; Don't feel bad Jordan), I have seen some protein sequences that people sent to the Blitz server. (I requested the help file hoping it would be intresting. It was :) Could someone quickly explain what the letters stand for? At first guess I thought amino acids but I'm 99.9% sure thats not what it is. :) Please pardon me for my extreme ignorance. ---Jason Burrell -- Jason_Burrell@fcircus.sat.tx.us Device Driver Stacker.sys not found. Hit (P) to panic! -- PGP public key available upon request. From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!SALK-SC2.SDSC.EDU!CLARK From: CLARK@SALK-SC2.SDSC.EDU (Steve Clark) Newsgroups: bionet.genome.chromosomes Subject: Salk Genome results available via WAIS and Gopher Message-ID: <9307010113.AA16349@net.bio.net> Date: 1 Jul 93 02:12:57 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 30 The results of the physical mapping project being carried out at the Salk Institute for Biological Studies are now accessible via WAIS and Gopher. The present data include mapping info and pcr conditions for STSs located on human chromosome 11. As more mapping and contiging results are finalized, they will be added to the WAIS server. These data are available from the WAIS database "Salk_Genome_Center" on rangersmith.sdsc.edu (192.31.153.23) and from the GDB Gopher server at merlot.welch.jhu.edu. To access it from the GDB Gopher server, first select "Genbank, PIR, Swiss_PROT and other Database Searches", then "Physical Mapping Data of Chromsome 11 (Salk)". Special thanks to Harry Mangalam at the Salk for implementing WAIS on our SGI, and to Dan Jacobson for pointing his GDB Gopher server at this WAIS database. Other Gopher server administrators are welcome to incorporate this WAIS database in their Gopher server if they like. Questions and comments regarding the contents of the database are welcome and should be directed to me. Sincerely, Stephen Clark, Ph.D clark@salk-sc2.sdsc.edu (Internet) Systems Analyst clark@salk (Bitnet) Molecular Genetics Lab The Salk Institute for Biological Studies P.O. Box 85800 (619) 453-4100 x451 (voice) San Diego, California (619) 558-9513 (fax) 92186-5800 USA From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!munnari.oz.au!constellation!aardvark.ucs.uoknor.edu!aardvark.ucs.uoknor.edu!broe From: broe@aardvark.ucs.uoknor.edu (Bruce Roe) Newsgroups: bionet.genome.chromosomes Subject: Re: What is the Human Genome Project?!?!? Message-ID: <1JUL199307223469@aardvark.ucs.uoknor.edu> Date: 1 Jul 93 12:22:00 GMT References: <9307010620.AA01dc5@fcircus.sat.tx.us> Distribution: bionet Organization: University of Oklahoma - University Computing Services Lines: 66 Nntp-Posting-Host: loopback.uoknor.edu News-Software: VAX/VMS VNEWS 1.41 Lines: 66 In article <9307010620.AA01dc5@fcircus.sat.tx.us>, Jason_Burrell@fcircus.sat.tx.us (Jason Burrell) writes... >....[Rest of message deleted to conserve bandwidth]... >> +--------------------------------------------------------------+ >> > >I would also like to know this. I am not a scientist, but a high-school >student who has been lucky enough to obtain a USENET account. I've been >reading this bionet group for a long time, but have posted exactly twice >(counting this time) :-) Genetics is one of my many hobbies.... How very exciting to see a high school student with a USENET account. >How can someone patent a gene? If this runs like everything else, I'll >be owned by some biological research corperation :-) Others already have answered this question earlier today. >Last but not least, (I am being a REAL ignoramus; Don't feel bad >Jordan), I have seen some protein sequences that people sent to the >Blitz server. (I requested the help file hoping it would be intresting. >It was :) Could someone quickly explain what the letters stand for? At >first guess I thought amino acids but I'm 99.9% sure thats not what it >is. :) >---Jason Burrell .. Jason_Burrell@fcircus.sat.tx.us Jason, Here is a list of the standard one-letter amino acid codes and their three-letter equivalents. The synonymous codons and their depiction in the IUB (International Union of Biochemistry) codes are shown. IUB Symbol 3-letter Meaning Codons Depiction A Ala Alanine GCT,GCC,GCA,GCG !GCX B Asp,Asn Aspartic, Asparagine GAT,GAC,AAT,AAC !RAY C Cys Cysteine TGT,TGC !TGY D Asp Aspartic GAT,GAC !GAY E Glu Glutamic GAA,GAG !GAR F Phe Phenylalanine TTT,TTC !TTY G Gly Glycine GGT,GGC,GGA,GGG !GGX H His Histidine CAT,CAC !CAY I Ile Isoleucine ATT,ATC,ATA !ATH K Lys Lysine AAA,AAG !AAR L Leu Leucine TTG,TTA,CTT,CTC,CTA,CTG !TTR,CTX,YTR;YTX M Met Methionine ATG !ATG N Asn Asparagine AAT,AAC !AAY P Pro Proline CCT,CCC,CCA,CCG !CCX Q Gln Glutamine CAA,CAG !CAR R Arg Arginine CGT,CGC,CGA,CGG,AGA,AGG !CGX,AGR,MGR;MGX S Ser Serine TCT,TCC,TCA,TCG,AGT,AGC !TCX,AGY;WSX T Thr Threonine ACT,ACC,ACA,ACG !ACX V Val Valine GTT,GTC,GTA,GTG !GTX W Trp Tryptophan TGG !TGG X Xxx Unknown !XXX Y Tyr Tyrosine TAT, TAC !TAY Z Glu,Gln Glutamic, Glutamine GAA,GAG,CAA,CAG !SAR * End Terminator TAA, TAG, TGA !TAR,TRA;TRR - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ Bruce A. Roe Professor of Chemistry and Biochemistry / / University of Oklahoma INTERNET: BROE@aardvark.ucs.uoknor.edu \ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!SALK-SC2.SDSC.EDU!CLARK From: CLARK@SALK-SC2.SDSC.EDU (Steve Clark) Newsgroups: bionet.genome.chromosomes Subject: Re: Salk Genome results available via WAIS and Gopher Message-ID: <9307012358.AA20382@net.bio.net> Date: 2 Jul 93 00:58:26 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 47 Rob Harper writes: /> Special thanks to Harry Mangalam at the Salk for implementing WAIS />on our SGI, and to Dan Jacobson for pointing his GDB Gopher server at this />WAIS database. Other Gopher server administrators are welcome to />incorporate this WAIS database in their Gopher server if they like. />Questions and comments regarding the contents of the database are welcome />and should be directed to me. / / I searched the directory-of-servers.src for "salk and harry" but / could not come up with any .src Has your WAIS .src been registered / with quake.think.com? Yes, they have it. In fact, you can try it out by logging onto their WAIS client (telnet to quake.think.com and log in as "wais"). / Would it be possible to have a copy of the .src posted here so that / gopher admins could incorporate it straight into their directories. Sure, I'll append it to the end of this message. Regards, Steve clark@salk-sc2.sdsc.edu (Internet) clark@salk (Bitnet) -------------------------------------------------------------------------- (:source :version 3 :ip-address "192.31.153.23" :ip-name "RANGERSMITH.SDSC.EDU" :tcp-port 210 :database-name "Salk_Genome_Center" :cost 0.00 :cost-unit :free :maintainer " Lori Romberg, Molecular Genetics Lab, Salk Institute (619) 453-4100, x451 romberg@molly.sdsc.edu" :description " This database contains the results of physical mapping of human chromosome 11, and other chromosomes, from the San Diego Genome Center at the Salk Institute.") From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!uwm.edu!math.ohio-state.edu!cs.utexas.edu!uunet!decwrl!decwrl!concert!news-feed-1.peachnet.edu!umn.edu!gaia.ucs.orst.edu!osshe.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!max.u.washington.edu!wijsman From: wijsman@max.u.washington.edu Newsgroups: bionet.genome.chromosomes Subject: Re: Paternity question Message-ID: <1993Jul1.095845.1@max.u.washington.edu> Date: 1 Jul 93 17:58:45 GMT Lines: 34 NNTP-Posting-Host: max.u.washington.edu >>If a man has A- blood, what are the blood types his offspring >>could have (not knowing the mother's blood type)? >Depending on the mother, his offspring could be A, AB, or O, all + or -. Don't forget B. If you don't know the mother's blood group, she could contribute any of the three alleles A, B, or O. The father, being A, could contribute either an A or and O (he could be AA or AO). Therefore, the 6 possible genotypes in the child, listing paternal allele first, are AA, AB, AO, OA, OB and OO. In terms of resulting blood types, the 6 genotypes correspond, respectively, to A, AB, A, A, B and O, or all 4 possible blood types. Therefore, without knowing the mother's blood type, in this example the paternal blood type will not exclude the father, no matter what the blood group of the child is. If the mother's blood type is known, then if the mother is A or O, a child who is AB or B will exclude the father. No other exclusions are possible with the A father and just one child. >>To be POSITIVE of who the father of a child is, what would be the >>next kinds of identification after the blood type? >"Molecular genetic fingerprinting" (from, say a blood sample) can exclude >almost all non-fathers. DNA fingerprinting can also put a very high probability on positive paternity, but nothing can identify the father with probability 1.0. Ellen Wijsman Div of Medical Genetics, RG-25 and Dept of Biostatistics University of Washington Seattle, WA 98195 wijsman@u.washington.edu (206) 543-8987 From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!wupost!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.genome.chromosomes Subject: Re: What is the Human Genome Project?!?!? Message-ID: Date: 1 Jul 93 12:53:50 GMT References: <9307010620.AA01dc5@fcircus.sat.tx.us> Distribution: bionet Lines: 38 Nntp-Posting-Host: husc10.harvard.edu Jason_Burrell@fcircus.sat.tx.us (Jason Burrell) writes: >In <9306290830.AA13323@net.bio.net>, jordan@netcom.com (Jordan A. Bortz) writes: >> Excuse me for being an ignoramus but: Don't use that word! There's nothing wrong with asking questions! >I have seen some protein sequences that people sent to the >Blitz server. (I requested the help file hoping it would be intresting. >It was :) Could someone quickly explain what the letters stand for? At >first guess I thought amino acids but I'm 99.9% sure thats not what it Yes, the letters stand for amino acids -- one letter per residue. Alanine Cysteine D=aspartic acid E=glutamic acid Glycine Histidine Isoleucine K=lysine Leucine Methionine asparagiNe Proline Q=glutamine aRginine Serine Threonine Valine tYrosine and, of course: Fenylalanine tWptophan :-) I strongly suggest you get a good biochemistry/molecular biology/genetics textbook -- it is a very worthwhile investment. Try a college bookstore, or there are several good ones available through Scientific American Books. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@biosun.harvard.edu From owner-chromosomes@net.bio.net Wed Jun 30 23:00:00 1993 Path: biosci!parc!decwrl!decwrl!uunet!mcsun!news.funet.fi!funic!convex!harper From: harper@convex.csc.FI (Rob Harper) Newsgroups: bionet.genome.chromosomes Subject: Re: Salk Genome results available via WAIS and Gopher Message-ID: <1993Jul1.084600.4860@nic.funet.fi> Date: 1 Jul 93 08:46:00 GMT References: <9307010113.AA16349@net.bio.net> Sender: usenet@nic.funet.fi Distribution: bionet Organization: Finnish Academic and Research Network Project - FUNET Lines: 27 Nntp-Posting-Host: convex.csc.fi In <9307010113.AA16349@net.bio.net> CLARK@SALK-SC2.SDSC.EDU (Steve Clark) writes: > Special thanks to Harry Mangalam at the Salk for implementing WAIS >on our SGI, and to Dan Jacobson for pointing his GDB Gopher server at this >WAIS database. Other Gopher server administrators are welcome to >incorporate this WAIS database in their Gopher server if they like. >Questions and comments regarding the contents of the database are welcome >and should be directed to me. I searched the directory-of-servers.src for "salk and harry" but could not come up with any .src Has your WAIS .src been registered with quake.think.com? Would it be possible to have a copy of the .src posted here so that gopher admins could incorporate it straight into their directories. Thanks in advance -=ROB=- -- Rob Harper E-mail: harper@convex.csc.fi Center for Scientific Computing Molbio/software: harper@nic.funet.fi Tietotie 6, P.O. Box 405 Telephone: +358 0 457 2076 SF-02101 Espoo Finland Fax: +358 0 457 2302