From owner-chromosomes@net.bio.net Thu Feb 03 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.intercon.com!psinntp!psinntp!psinntp!vaxa.hofstra.edu!vaxa.hofstra.edu!mloughran1 Newsgroups: sci.bio,bionet.molbio.genome-program,bionet.genome.chromosomes Subject: Message-ID: <1994Feb1.140536.1@vaxa> From: mloughran1@vaxa.hofstra.edu (MATTHEW J. LOUGHRAN) Date: 1 Feb 94 14:05:36 EST References: <2grtau$62m@sugar.NeoSoft.COM> <1994Jan10.225607.16218@genethon.fr> Distribution: world Organization: Hofstra University Nntp-Posting-Host: vaxb.hofstra.edu Lines: 46 Xref: biosci sci.bio:6345 bionet.molbio.genome-program:648 bionet.genome.chromosomes:170 q ==q q In article , robison1@husc10.harvard.edu (Keith Robison) writes: > It's been obvious from the start that the CEPH/Genethon people had a > good Internet scheme going -- access by all the favorite protocols. > (and to make things even better, the good folks at the U.Michigan > Genome Center have provided WWW search facilities. > Human Genome Physical Map from CEPH-Genethon (at U.Michigan Genome Center) > > But what is the explanation for the Cohen quote in the Science article > about "only 1 person sending out requests on the Internet"? Was some > important context lost? Did Dr. Cohen mean that there was one person > available for non-internet requests or for showing non-netliterate > biologists how to get the data? The incongruence between that article > and the excellent (and well net-publicized) net access has had me wondering > for days. > > Hope someone can shed some light on this curious statement. > > Keith Robison > Harvard University > Department of Cellular and Developmental Biology > Department of Genetics / HHMI > q > krobison@nucleus.harvard.edu > q > > From owner-chromosomes@net.bio.net Sun Feb 06 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!msuinfo!netnews.upenn.edu!amalthea.humgen.upenn.edu!tisdall From: tisdall@amalthea.humgen.upenn.edu (James Tisdall) Newsgroups: bionet.genome.chromosomes Subject: search by chromosome Date: 7 Feb 1994 19:05:00 GMT Organization: University of Pennsylvania Lines: 33 Message-ID: <2j63cs$iik@netnews.upenn.edu> NNTP-Posting-Host: amalthea.humgen.upenn.edu The internet service DNA WorkBench (software available for unix and mac at ftp site cbil.humgen.upenn.edu:/pub/dnaworkbench) has a new, undocumented feature - the command chromosome 22 searches GDB and GenBank for everything it can find on the human chromosome named. You can add an organism name such as chromosome 4 rattus This just searches in GenBank. The results are quite good, but not perfect - for 22 it has no false positives, but misses at least one. Spot checks of other human chromosomes seem similar. Only the version of the program just placed into the ftp site supports this lookup. Comments welcome - I'd like to improve it. (A later post will present some interesting findings on the lack of overlap between GDB and GenBank.) Jim ====================================================================== James Tisdall Departments of Genetics and Computer and Information Science Computational Biology and Informatics Laboratory, Human Genome Project University of Pennsylvania tisdall@cbil.humgen.upenn.edu 215-573-3113 ====================================================================== From owner-chromosomes@net.bio.net Wed Feb 09 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!sdd.hp.com!spool.mu.edu!agate!msuinfo!netnews.upenn.edu!amalthea.humgen.upenn.edu!tisdall From: tisdall@amalthea.humgen.upenn.edu (James Tisdall) Newsgroups: bionet.genome.chromosomes Subject: GenBank entries by chromosome Date: 10 Feb 1994 03:45:00 GMT Organization: University of Pennsylvania Lines: 379 Distribution: world Message-ID: <2jcajs$9qo@netnews.upenn.edu> NNTP-Posting-Host: amalthea.humgen.upenn.edu ################################################################ Finding all GenBank entries for a given human chromosome. ################################################################ ######## Summary: ######## We've found that it is necessary to search both GDB and GenBank, since there seems to be significant non-overlap. For human chromosome 22, we find 279 entries with a search of GenBank annotations as described below, and 301 entries with a search of GDB as described below. We then find that only 147 entries are in the overlap (intersection), and 286 are not, making a total of 433 unique entries. 301 GDB 279 GenBank 147 Overlap (intersection) 286 Not in overlap (132 in GenBank not in GDB, 154 in GDB not in GenBank) 433 Total human chromosome 22 (union of GDB and GenBank searches) The results for all chromosomes are included at the end of this document. ########### Discussion: ########### Although we don't claim 100% accuracy, and expect some false positives and negatives, the results are still striking. The norm is for less than 50% overlap between the GenBank annotations as found with DNA WorkBench, and the GDB mapping information. Similarly, a significant fraction of results are missed by relying on only one or the other method. See the complete results below. Assuming our results are accurate, then clearly there is room for better integration between GDB and GenBank chromosome location information. Perhaps our methods may be of some use to the database maintainers, as a tool to enhance the integration. We are now providing this search as a command "chromosome" in DNA WorkBench. The compute intensive nature of the search led us to precompute the chromosome information for humans and store it in a fast-access index. Thus a query completes in seconds. The index information is updated regularly by automation. ################### Details of searches ################### ####### GenBank ####### To search for the GenBank annotations, we use the program DNA WorkBench with the following commands: (DNA WorkBench is an internet service, software for Unix and Mac (and PC) at anonymous ftp location cbil.humgen.upenn.edu:/pub/dnaworkbench) # # DNA WorkBench script to get list of human genes on chromosome 22 in GenBank # database genbank text "chromosome 22\D" gball gbnew text \/map="22\D gball gbnew text \/chromosome="22\D gball gbnew # the next one works okay for human chromosome 22, but may generate some # false positives for other chromosomes text \b22[pq][^a-z] gball gbnew union 1 2 3 4 organism sapiens intersection 5 6 This search (plus the one on GDB) now may be executed simply as # # DNA WorkBench script for human chromosomes using precomputed index # (N.B. need most recent version of software, Unix available 2/9/94, Mac soon) # chromosome 22 In general, this seems to work quite well; however, we have found at least one GenBank entry that is on chromosome 22 and not found by this search (nor by the GDB search below); there may well be others. We do not seem to be getting any false positives; but applied to another chromosome, there may be some false positives. The size of the GenBank human entries (about 50000) precludes our checking all results for all chromosomes. We are eager to learn of such cases, so as to improve our search procedure. The program DNA WorkBench does a complete search (in parallel) of all the GenBank entries. The text being searched for can be specified as a "regular expression". The "wildcards" used here are \/ to represent / \D to represent a non-digit [pq] to represent p or q [^a-z] to represent a non-letter. (Case insensitive). Thus, the DNA WorkBench search of GenBank is a search for GenBank annotations specifying the chromosome location. (See the "help regular" command in DNA WorkBench for details.) ####### GDB ####### To search GDB, we use the following Sybase command (by Barbara Eckman): $sql_cmd= "select distinct locus_symbol, genbank_ref from locus, object_genbank_eref, locus_cyto_location where locus.locus_id = locus_cyto_location.locus_id and locus.locus_id = object_genbank_eref.object_id and object_class_key = 1 and loc_cyto_chrom_num = '22' UNION select distinct locus_symbol, genbank_ref from probe, probe_locus_iref, locus, object_genbank_eref, locus_cyto_location where probe.probe_id = probe_locus_iref.probe_id and probe_locus_iref.locus_id = locus.locus_id and locus.locus_id = locus_cyto_location.locus_id and probe.probe_id = object_genbank_eref.object_id and object_class_key = 2 and loc_cyto_chrom_num = '22' order by locus_symbol desc"; We then read in the list of accession numbers obtainable from this search, and compare with the GenBank search: # # DNA WorkBench script continued # N.B. only latest version supports "gdb" command # gdb chromosome 22 union 7 8 #this prints out a list of one-line headers: headers 1-$ #this writes the list of one-line headers to a file: headers 1-$ write chromo_22_headers #see also "help searches" for writing list of accession numbers (Again, the new "chromosome 22" command does all this much faster.) ######################################################## Here are the results for all human chromosomes. The first three lines are the result of running the "chromosome 22" (e.g.) command. The third (union) line shows the total GenBank entries for the chromosome as found by GDB and GenBank (as per DNA WorkBench) searches. The fourth (intersection) line shows the size of the overlap. The fifth line shows GenBank (DNA WorkBench) results that are not in GDB; the sixth line shows GDB results that are not in GenBank (DNA WorkBench). Size Number Command _____________________________________ 986 1 chromosome 1 (in genbank) 1356 2 chromosome 1 (in gdb) 1688 3 union $ $-1 654 4 intersect 1 2 332 5 difference 1 2 702 6 difference 2 1 Size Number Command _____________________________________ 789 1 chromosome 2 (in genbank) 909 2 chromosome 2 (in gdb) 1221 3 union $ $-1 477 4 intersect 1 2 312 5 difference 1 2 432 6 difference 2 1 Size Number Command _____________________________________ 435 1 chromosome 3 (in genbank) 581 2 chromosome 3 (in gdb) 713 3 union $ $-1 303 4 intersect 1 2 132 5 difference 1 2 278 6 difference 2 1 Size Number Command _____________________________________ 1376 1 chromosome 4 (in genbank) 1366 2 chromosome 4 (in gdb) 1625 3 union $ $-1 1117 4 intersect 1 2 259 5 difference 1 2 249 6 difference 2 1 Size Number Command _____________________________________ 409 1 chromosome 5 (in genbank) 478 2 chromosome 5 (in gdb) 628 3 union $ $-1 259 4 intersect 1 2 150 5 difference 1 2 219 6 difference 2 1 Size Number Command _____________________________________ 1015 1 chromosome 6 (in genbank) 1058 2 chromosome 6 (in gdb) 1507 3 union $ $-1 566 4 intersect 1 2 449 5 difference 1 2 492 6 difference 2 1 Size Number Command _____________________________________ 1024 1 chromosome 7 (in genbank) 1115 2 chromosome 7 (in gdb) 1455 3 union $ $-1 684 4 intersect 1 2 340 5 difference 1 2 431 6 difference 2 1 Size Number Command _____________________________________ 396 1 chromosome 8 (in genbank) 495 2 chromosome 8 (in gdb) 583 3 union $ $-1 308 4 intersect 1 2 88 5 difference 1 2 187 6 difference 2 1 Size Number Command _____________________________________ 483 1 chromosome 9 (in genbank) 419 2 chromosome 9 (in gdb) 698 3 union $ $-1 204 4 intersect 1 2 279 5 difference 1 2 215 6 difference 2 1 Size Number Command _____________________________________ 401 1 chromosome 10 (in genbank) 522 2 chromosome 10 (in gdb) 629 3 union $ $-1 294 4 intersect 1 2 107 5 difference 1 2 228 6 difference 2 1 Size Number Command _____________________________________ 598 1 chromosome 11 (in genbank) 699 2 chromosome 11 (in gdb) 963 3 union $ $-1 334 4 intersect 1 2 264 5 difference 1 2 365 6 difference 2 1 Size Number Command _____________________________________ 410 1 chromosome 12 (in genbank) 584 2 chromosome 12 (in gdb) 689 3 union $ $-1 305 4 intersect 1 2 105 5 difference 1 2 279 6 difference 2 1 Size Number Command _____________________________________ 270 1 chromosome 13 (in genbank) 271 2 chromosome 13 (in gdb) 356 3 union $ $-1 185 4 intersect 1 2 85 5 difference 1 2 86 6 difference 2 1 Size Number Command _____________________________________ 1018 1 chromosome 14 (in genbank) 1060 2 chromosome 14 (in gdb) 1545 3 union $ $-1 533 4 intersect 1 2 485 5 difference 1 2 527 6 difference 2 1 Size Number Command _____________________________________ 205 1 chromosome 15 (in genbank) 263 2 chromosome 15 (in gdb) 345 3 union $ $-1 123 4 intersect 1 2 82 5 difference 1 2 140 6 difference 2 1 Size Number Command _____________________________________ 250 1 chromosome 16 (in genbank) 317 2 chromosome 16 (in gdb) 408 3 union $ $-1 159 4 intersect 1 2 91 5 difference 1 2 158 6 difference 2 1 Size Number Command _____________________________________ 608 1 chromosome 17 (in genbank) 541 2 chromosome 17 (in gdb) 876 3 union $ $-1 273 4 intersect 1 2 335 5 difference 1 2 268 6 difference 2 1 Size Number Command _____________________________________ 198 1 chromosome 18 (in genbank) 192 2 chromosome 18 (in gdb) 252 3 union $ $-1 138 4 intersect 1 2 60 5 difference 1 2 54 6 difference 2 1 Size Number Command _____________________________________ 497 1 chromosome 19 (in genbank) 630 2 chromosome 19 (in gdb) 879 3 union $ $-1 248 4 intersect 1 2 249 5 difference 1 2 382 6 difference 2 1 Size Number Command _____________________________________ 178 1 chromosome 20 (in genbank) 273 2 chromosome 20 (in gdb) 306 3 union $ $-1 145 4 intersect 1 2 33 5 difference 1 2 128 6 difference 2 1 Size Number Command _____________________________________ 485 1 chromosome 21 (in genbank) 365 2 chromosome 21 (in gdb) 558 3 union $ $-1 292 4 intersect 1 2 193 5 difference 1 2 73 6 difference 2 1 Size Number Command _____________________________________ 279 1 chromosome 22 (in genbank) 301 2 chromosome 22 (in gdb) 433 3 union $ $-1 147 4 intersect 1 2 132 5 difference 1 2 154 6 difference 2 1 Size Number Command _____________________________________ 1030 1 chromosome X (in genbank) 860 2 chromosome X (in gdb) 1362 3 union $ $-1 528 4 intersect 1 2 502 5 difference 1 2 332 6 difference 2 1 Size Number Command _____________________________________ 68 1 chromosome Y (in genbank) 35 2 chromosome Y (in gdb) 89 3 union $ $-1 14 4 intersect 1 2 54 5 difference 1 2 21 6 difference 2 1 ====================================================================== James Tisdall Departments of Genetics and Computer and Information Science Computational Biology and Informatics Laboratory Human Genome Project for Chromosome 22, University of Pennsylvania and Childrens Hospital of Philadelphia tisdall@cbil.humgen.upenn.edu 215-573-3113 ====================================================================== From owner-chromosomes@net.bio.net Wed Feb 09 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: kristoff@net.bio.net (David Kristofferson) Newsgroups: bionet.genome.chromosomes Subject: IMPORTANT BIOSCI INFORMATION Date: 10 Feb 1994 10:04:59 -0000 Lines: 244 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2jd0sb$dbd@mserv1.dl.ac.uk> Original-To: biochrom@net.bio.net 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 or for retrieval by gopher to net.bio.net, port 70. 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 your 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 serves as a directory that enables 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 is reindexed nightly 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 is 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. 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. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) 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. The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the USENET name even if you don't participate by e-mail. WAIS might get confused by the periods in the USENET names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group. For example: comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below ---- NOT the USENET names below MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIO-SOFTWARE bionet.software CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast Listing newsgroups on the comment: line is optional, of course. 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 Feb 10 22:00:00 1994 Newsgroups: bionet.general,bionet.genome.chromosomes,bionet.molbio.genome-program,bionet.software,comp.infosystems.www,embnet.general,fr.bio.general Path: biosci!bcm!cs.utexas.edu!math.ohio-state.edu!jussieu.fr!univ-lyon1.fr!julienas!genethon!claude From: hugemap@genethon.fr Subject: Genethon's Physical Map WWW server Message-ID: <1994Feb11.185750@genethon.fr> Originator: claude@icare.genethon.fr Sender: news@genethon.fr Nntp-Posting-Host: icare.genethon.fr Organization: Genethon -- Human Genome Research Centre Date: Fri, 11 Feb 1994 17:57:50 GMT Lines: 64 Xref: biosci bionet.general:7723 bionet.genome.chromosomes:174 bionet.molbio.genome-program:656 bionet.software:7231 comp.infosystems.www:4941 Announcing Genethon's Human Physical Map Data WWW server This server is an experimental WWW interface to the public part of the physical map database hugemap. It is implemented on top of IDB, an object-oriented persistent environment developped at Genethon for this purpose. The data on clones or STSs can be accessed through Dnumbers, AFM names (for STSs) or CEPH names (or UNIX-style regular expressions matching one of these formats). It is the same (except for more frequent updates) as that available on ceph-genethon-map ftp server, thus you can find: * for STSs: - screening results, with both positive (individually verified or unique) and individually negative clones. - for those clones, other STSs tested and chromosomal assignment through Alu-PCR product hybridization. * for clones: - screening results. - chromosomal assignment through Alu-PCR product hybridization. - potentially overlapping clones, as deduced from L1 and THE fingerprints and Alu-PCR product hybridization. Additionally, this server provides: * links toward the GDB gopher server for clones or STSs that have Dnumbers. * links toward Genethon's Human Genetic Map Data wais server for Genethon's microsatellites: this server contains full sequence for those STSs. Those links are, of course, hypertext links, i.e. are accessible through clicking on object names. For more information and/or data and/or fun, just aim your favourite mosaic client at URL : http://www.genethon.fr and click on "CEPH/Genethon Physical Map" or directly load: http://www.genethon.fr/genethon_fr.html (french page) http://www.genethon.fr/genethon_en.html (english page) Any feedback, comment or suggestion welcome at hugemap@genethon.fr hugemap team (Eric Viara, Stuart Pook, Emmanuel Barillot, Bruno Lacroix) 13, place de Rungis 75013 Paris tel: (33 1) 44-16-27-20 (PPF) fax: (33 1) 45-88-52-20 email: hugemap@genethon.fr -- ------------------------------------------------------------------------------ Claude Scarpelli Internet : claude@genethon.fr Human Polymorphism Study Center or : claude@cephb.fr From owner-chromosomes@net.bio.net Fri Feb 11 22:00:00 1994 Path: biosci!NET.BIO.NET!biosci-help From: biosci-help@NET.BIO.NET (BIOSCI Administrator) Newsgroups: bionet.genome.chromosomes Subject: test of biochrom@net.bio.net Date: 12 Feb 1994 02:27:24 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 2 Sender: daemon@net.bio.net Distribution: bionet Message-ID: Reply-To: biosci-help@net.bio.net NNTP-Posting-Host: net.bio.net test of biochrom@net.bio.net From owner-chromosomes@net.bio.net Mon Feb 14 22:00:00 1994 Path: biosci!parc!decwrl!ames!sgiblab!sdd.hp.com!saimiri.primate.wisc.edu!news.doit.wisc.edu!fout.nic.wisc.edu!user From: wwang@macc.wisc.edu (Wensheng Wang) Newsgroups: bionet.genome.chromosomes Subject: Re: test of biochrom@net.bio.net Followup-To: bionet.genome.chromosomes Date: Mon, 14 Feb 1994 21:46:04 -0600 Organization: University of Wisconsin at Madison, USA Lines: 12 Distribution: bionet Message-ID: References: NNTP-Posting-Host: 144.92.180.48 In article , biosci-help@NET.BIO.NET (BIOSCI Administrator) wrote: > > test of biochrom@net.bio.net Also a test. -- -------------------------------------------------------------------------- Wensheng Wang Tel: (608)-262-6591 University of Wisconsin at Madison Email: wwang@macc.wisc.edu -------------------------------------------------------------------------- From owner-chromosomes@net.bio.net Wed Feb 16 22:00:00 1994 Newsgroups: bionet.genome.chromosomes Path: biosci!daresbury!doc.ic.ac.uk!warwick!str-ccsun!strath-cs!bnr.co.uk!pipex!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!raven.bio.indiana.edu!user From: lwashing@sunflower.bio.indiana.edu (Lawrence Washington) Subject: Automated DNA Sequencing Core Lab Message-ID: Followup-To: bionet.genome.chromosomes Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: raven.bio.indiana.edu Organization: Indiana University Date: Thu, 17 Feb 1994 15:56:51 GMT Lines: 30 I gather that this is the chartered location for discussions on automated DNA sequencing. IÕm a total rookie in the field and would enjoy reading other peopleÕs wisdom. Maybe this will get something going. We are about to launch a DNA sequencing service at our small biotech core lab and could use some advice from those of you who are experienced. (Have you ever been experienced?) This is strictly in-house for our biology department (not a commercial endeavor). We will be using an automated fluorescent-based system (to be installed at the end of March) (_not_ the brand you probably assume, but I expect they are all somewhat comparable). I have a couple of questions; 1) How much to charge users? The machine is paid for, but we need to cover operating costs and pay a part time tech. (After a few months of operation and careful record keeping we should have an idea, but where is a good place to start?) 2) We plan to have customers do their own sample preps (to keep our costs down.) Is that a mistake? Are sample conditions so particular that we should plan to handle that part ourselves? 3) How long until you were up and running with the new system? Thanks for your advice. Lawrence Washington Indiana Institute for Molecular and Cellular Biology Indiana University,Bloomington lwashing@sunflower.bio.indiana.edu From owner-chromosomes@net.bio.net Wed Feb 16 22:00:00 1994 Path: biosci!GALAXY.GOV.BC.CA!A1FETCHER From: A1FETCHER@GALAXY.GOV.BC.CA (ALLIN1 Fetcher) Newsgroups: bionet.genome.chromosomes Subject: Automated DNA Sequencing Core Lab Date: 17 Feb 1994 23:48:34 -0000 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 64 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <01H8ZX3T1RSGC1BCE6@mr.gov.bc.ca> NNTP-Posting-Host: net.bio.net --Boundary (ID exKgrVyLageirlp49J4fXw) Content-type: TEXT/PLAIN; CHARSET=US-ASCII Due to a mail delivery problem this morning, the attached message was not delivered directly to your account. However, it has been forwarded to you by the automated ALL-IN-1 postoffice. Please do not use the ANSWER command to reply to this note. Instead, use the FORWARD command to re-address it to the original sender. Sorry for the inconvenience. ALL-IN-1 Postoffice (389-3200) --Boundary (ID exKgrVyLageirlp49J4fXw) MIME-version: 1.0 Content-type: MESSAGE/RFC822 Date: Thu, 17 Feb 1994 07:56:00 PST Subject: Automated DNA Sequencing Core Lab Sender: "news@usenet.ucs.indiana.edu" To: "biochrom@net.bio.net" Content-type: TEXT/PLAIN; CHARSET=US-ASCII Posting-date: Thu, 17 Feb 1994 00:00:00 PST Importance: normal A1-type: MAIL I gather that this is the chartered location for discussions on automated DNA sequencing. IUm a total rookie in the field and would enjoy reading other peopleUs wisdom. Maybe this will get something going. We are about to launch a DNA sequencing service at our small biotech core lab and could use some advice from those of you who are experienced. (Have you ever been experienced?) This is strictly in-house for our biology department (not a commercial endeavor). We will be using an automated fluorescent-based system (to be installed at the end of March) (_not_ the brand you probably assume, but I expect they are all somewhat comparable). I have a couple of questions; 1) How much to charge users? The machine is paid for, but we need to cover operating costs and pay a part time tech. (After a few months of operation and careful record keeping we should have an idea, but where is a good place to start?) 2) We plan to have customers do their own sample preps (to keep our costs down.) Is that a mistake? Are sample conditions so particular that we should plan to handle that part ourselves? 3) How long until you were up and running with the new system? Thanks for your advice. Lawrence Washington Indiana Institute for Molecular and Cellular Biology Indiana University,Bloomington lwashing@sunflower.bio.indiana.edu --Boundary (ID exKgrVyLageirlp49J4fXw)-- From owner-chromosomes@net.bio.net Wed Feb 16 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!agate!msuinfo!harbinger.cc.monash.edu.au!uniwa!newsman!Jim.Cummins From: cummins@possum.murdoch.edu.au (Jim Cummins) Newsgroups: bionet.genome.chromosomes Subject: Chromosome number for Dolphins Date: 17 Feb 1994 01:22:25 GMT Organization: Murdoch University, Western Australia Lines: 10 Sender: -Not-Authenticated-[6523] Message-ID: <2jugshINN5f3@newsman.csu.murdoch.edu.au> NNTP-Posting-Host: vetmac3.csu.murdoch.edu.au X-Posted-From: InterNews 1.0@newsman.csu.murdoch.edu.au. Xdisclaimer: No attempt was made to authenticate the sender's name. Anyone know the chromosome number for any species in the family Delphinidae? Or can point me at a source reference? Thanks Jim Cummins School of Veterinary Studies Murdoch University Western Australia 6150 Tel +61-9-360 2668 Fax +61-9-310 4144 "An inordinate fondness for Beetles" From owner-chromosomes@net.bio.net Thu Feb 17 22:00:00 1994 Newsgroups: bionet.genome.chromosomes Path: biosci!headwall.Stanford.EDU!agate!howland.reston.ans.net!cs.utexas.edu!uunet!psinntp!hk.super.net!uxmail!hpg30a.csc.cuhk.hk!hkuxb.hku.hk!hkucc.hku.hk!xfcheung From: xfcheung@hkucc.hku.hk Subject: exut Message-ID: <1994Feb18.231136.1@hkucc.hku.hk> Lines: 13 Sender: usenet@hkuxb.hku.hk (USENET News System) Nntp-Posting-Host: hkucc.hku.hk Organization: The University of Hong Kong Date: Fri, 18 Feb 1994 15:11:36 GMT Hi, I have one question Why pulse field gel electrophoresis could seperate greater piece of genetic material compared with the conventional gel electrophereis. In the past I always thought that pulse field gel electrophoresis was better because it is more sensitive to seperating chromoasomes so that help sorting. Why it can seperate larger DNA than conventional electrphoresis David Chiu From owner-chromosomes@net.bio.net Sun Feb 20 22:00:00 1994 Path: biosci!daresbury!not-for-mail From: "Stefan Vetter" Newsgroups: bionet.genome.chromosomes Subject: heredity Date: 21 Feb 1994 14:14:38 -0000 Organization: Vet.Med.Uni Wien Lines: 7 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2kafke$g21@mserv1.dl.ac.uk> Original-To: biochrom@dl.ac.uk Hello, I am looking for a forum for disputation and discussion of the heredity of different characters (i.e. morphological, physiological, cytological &c) within plants (natural and artificial hybrids). Am I right here? SteVe Stefan.Vetter@vu-wien.ac.at From owner-chromosomes@net.bio.net Wed Feb 23 22:00:00 1994 Newsgroups: bionet.genome.chromosomes Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!torn!nott!uotcsi2!news From: 055132@engnov.genie.uottawa.ca (WEIGUO ZHAN) Subject: Re: heredity Message-ID: <055132.1.0@engnov.genie.uottawa.ca> Lines: 11 Sender: news@csi.uottawa.ca Nntp-Posting-Host: 137.122.21.153 Organization: Faculty of Engineering, University of Ottawa. References: <2kafke$g21@mserv1.dl.ac.uk> Distribution: bionet Date: Thu, 24 Feb 94 01:05:10 GMT In article <2kafke$g21@mserv1.dl.ac.uk> "Stefan Vetter" writes: >From: "Stefan Vetter" >Subject: heredity >Date: 21 Feb 1994 14:14:38 -0000 >Hello, >I am looking for a forum for disputation and discussion of the heredity of different >characters (i.e. morphological, physiological, cytological &c) within plants >(natural and artificial hybrids). >Am I right here? >SteVe >Stefan.Vetter@vu-wien.ac.at From owner-chromosomes@net.bio.net Wed Feb 23 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!news.msfc.nasa.gov!sol.ctr.columbia.edu!news.kei.com!yeshua.marcam.com!charnel!olivea!decwrl!decwrl!usenet.coe.montana.edu!CIS.NMCLITES.EDU!trumpet-user From: trumpet-user@CIS.NMCLITES.EDU (Default Trumpet User) Newsgroups: bionet.genome.chromosomes Subject: Hello? Date: Thu, 24 Feb 1994 18:20:05 GMT Organization: Norther Montana College Lines: 1 Message-ID: NNTP-Posting-Host: 192.150.88.202 Hello!