From owner-embldatabank@net.bio.net Thu Aug 11 23:00:00 1994 Path: biosci!internet!biosci!not-for-mail From: kristoff (David Kristofferson) Newsgroups: bionet.molbio.embldatabank Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 12 Aug 1994 02:02:17 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 322 Sender: daemon@net.bio.net Distribution: world Message-ID: <199408120900.CAA09936@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. IF YOU ARE LOCATED IN THE AMERICAS OR PACIFIC RIM COUNTRIES, please send a message to biosci@net.bio.net Instructions will be returned automatically, so the contents of your message do not matter. IF YOU ARE LOCATED IN EUROPE, AFRICA OR CENTRAL ASIA, please send a message to MXT@dl.ac.uk containing the word help in the body of the message to retrieve e-mail server instructions. Any text placed on the Subject: line of your message will be ignored, so be sure to put the "help" command in the body of the message. If you need personal assistance, a BIOSCI staff member can be contacted at either of the following addresses. Please contact the address designated for your location. Support Address Location --------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci-help@net.bio.net Americas and the Pacific Rim **** SEARCHING BIOSCI ARCHIVES **** The easiest way to search the BIOSCI archives is to use gopher software and connect over the Internet to net.bio.net, the U.S. BIOSCI computer. We maintain three indexes which are searchable from the main gopher menu on net.bio.net: (1) an index of all BIOSCI postings; (2) an index of individual journal article references from the Table of Contents postings on the BIO-JOURNALS newsgroup; and (3) an index of BIOSCI users including regular mail and e-mail addresses, phone/FAX numbers, research interests, and newsgroup participation. 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 (anything entered on the Subject: line is ignored). WAIS software can also be used to search the archives as described in the BIOSCI FAQ (see below). Finally, the BIOSCI archive files are accessible by anonymous FTP to net.bio.net [134.172.2.69] in the directory pub/BIOSCI. **** 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/doc/biosci.FAQ or for retrieval by gopher to net.bio.net, port 70. It may also be requested by sending the command info faq in the body of an e-mail message to the Internet address biosci-server@net.bio.net. Please do not enter the info faq command on the Subject: line of your message since the e-mail server ignores text on the Subject: line. 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, waismail, and gopher access. If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. 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. 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). PLEASE DO NOT alter any of the field identifiers such as "first name: ". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question. 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., 15-05-93 for 15 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., 15-05-93, not 15-5-93. 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 BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CYTONET bionet.cellbiol.cytonet 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 GRASSES-SCIENCE bionet.biology.grasses 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 MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STRUCTURAL-NMR bionet.structural-nmr 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-embldatabank@net.bio.net Thu Aug 11 23:00:00 1994 Path: biosci!rutgers!gatech!howland.reston.ans.net!pipex!lyra.csx.cam.ac.uk!doc.ic.ac.uk!charlie.lif.icnet.uk!news.lif.icnet.uk!alex From: alex@darwin.lif.icnet.uk (Alex Whittaker - BIU) Newsgroups: bionet.molbio.embldatabank Subject: EMBL locus name to Accession Number Date: 12 Aug 1994 14:55:54 GMT Organization: Imperial Cancer Research Fund Lines: 31 Distribution: world Message-ID: NNTP-Posting-Host: darwin.lif.icnet.uk Hi, I am trying to make a small GCG database containing all sequence entries described in the eukaryote promoter database (EPD). I have pulled out 60% of the sequences from our GenBank databases, unfortunately however, the remainder have EMBL locus names not common with the genbank entries in our local sets. What would solve this problem would be a utility to change EMBL locus names into accession numbers, or a database retrieval program into which I can feed a file of 1200 locus names. Regards, Alex Whittaker ______ \||/_ | | oo \ "All I know Biomedical Informatics Unit | | L_ is that I know Imperial Cancer Research Fund |______| \/ nothing" London ________ | [========] / alex@bison.lif.icnet.uk ---OOO- |ooooooo| -- Alex Whittaker ______ \||/_ | | oo \ "All I know Biomedical Informatics Unit | | L_ is that I know Imperial Cancer Research Fund |______| \/ nothing" London ________ | [========] / alex@bison.lif.icnet.uk ---OOO- |ooooooo| From owner-embldatabank@net.bio.net Wed Aug 17 23:00:00 1994 Path: biosci!agate!doc.ic.ac.uk!daresbury!not-for-mail From: Paul Britton (Tel \(44\) \(0\)635 578411) Newsgroups: bionet.molbio.embldatabank Subject: How to access Geneseq Database Date: 18 Aug 1994 17:15:38 +0100 Lines: 31 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <3301fa$sb2@mserv1.dl.ac.uk> Sensitivity: Company-Confidential Original-To: virology@dl.ac.uk (Receipt Notification Requested) (Non Receipt Notification Requested) (Reply Requested), embl-database@dl.ac.uk (Receipt Notification Requested) (Non Receipt Notification Requested) (Reply Requested) ------------------------------ Start of body part 1 Hi I would like to obtain a copy of a sequence from the Geneseq Database. An accession number was cited in a recent paper. Any help would be appreciated. Cheers Paul Britton ------------------------------ Start of body part 2 ******************************************************************************* * Paul Britton | Tel : (44) 635 577268 * * Division of Molecular Biology | Fax : (44) 635 577263 * * Institute for Animal Health | Janet : Paul.Britton@bbsrc.ac.uk * * Compton Laboratory | X.400 : G=Paul; S=Britton; O=BBSRC; * * Compton | P=uk.ac; C=GB * * Newbury, Berkshire | * * RG16 0NN, UK | * * | * * // \\ // \\ // \\ // \\ // \\ // \\ // \\ * * | \\ // | :,\\': | \\ // | :,\\': | \\ // | :,\\': | \\ * * | | \\ // | | // \\ | | \\ // | | // \\ | | \\ // | | // \\ | | * * \\ | :,\\': | // \\ | :,\\': | // \\ | :,\\': | // \\ | * * \\ // \\ // \\ // \\ // \\ // \\ // \\ * *******************************************************************************  ------------------------------ End of body part 2 From owner-embldatabank@net.bio.net Thu Aug 18 23:00:00 1994 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de (Peter Stoehr) Newsgroups: bionet.molbio.embldatabank Subject: Re: How to access Geneseq Database Message-ID: <1994Aug19.203038.171492@eros.embl-heidelberg.de> Date: 19 Aug 94 20:30:38 +0100 References: <3301fa$sb2@mserv1.dl.ac.uk> Distribution: bionet Organization: European Molecular Biology Laboratory Lines: 17 In article <3301fa$sb2@mserv1.dl.ac.uk>, Paul Britton (Tel \(44\) \(0\)635 578411) writes: > > Hi > I would like to obtain a copy of a sequence from the Geneseq Database. An > accession number was cited in a recent paper. Any help would be appreciated. > Paul, GeneSeq is a database of sequences extracted from the patent literature which is commercial product of Intelligenetics & Derwent. You either have to buy the database, or hope some kind soul who already has will send you the sequence. If the article happened to quote the patent number, we might be able to find it here. Regards, Peter Stoehr EMBL Data Library From owner-embldatabank@net.bio.net Sat Aug 20 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!news.ecn.bgu.edu!psuvax1!news.pop.psu.edu!news.cac.psu.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: cc37@cornell.edu (CC) Newsgroups: bionet.molbio.embldatabank Subject: protein info?? Followup-To: bionet.molbio.embldatabank Date: 21 Aug 1994 22:05:10 GMT Organization: Cornell University Lines: 10 Sender: cc37@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: 132.236.171.160 Hi -- Do there exist databases that have information such as secondary & tertiary structures, active sites, mutations that disrupt function, etc., for highly-conserved proteins? I am particularly interested in ATP synthase FO subunits, cytochrome c oxidase subunits, and other H+ pore-forming proteins. So far I've just been searching through the literature, and if I could access fairly complete information on line, this would be a great leap forward for my dissertation. Any help is appreciated, and please send e-mail to cc37@cornell.edu. Thanks! -- CC From owner-embldatabank@net.bio.net Mon Aug 22 23:00:00 1994 Newsgroups: bionet.molbio.embldatabank Path: biosci!agate!howland.reston.ans.net!EU.net!sunic!news.lth.se!news.lu.se!bosse-q840.wblab.lu.se!Bo.Servenius From: Bo Servenius Subject: Size and release info for EMBL 39 Message-ID: <1994Aug23.142956.18693@nomina.lu.se> X-Xxmessage-Id: X-Xxdate: Tue, 23 Aug 94 16:24:42 GMT Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: bosse-q840.wblab.lu.se Organization: Lund university, Sweden X-Useragent: Version 1.1.3 Date: Tue, 23 Aug 1994 14:29:56 GMT Lines: 7 Dear Netters: Could ylu please point me to info about the size and releasedate of EMBL v39. yours BOSSE From owner-embldatabank@net.bio.net Mon Aug 22 23:00:00 1994 Newsgroups: bionet.molbio.embldatabank Path: biosci!agate!doc.ic.ac.uk!daresbury!bioftp.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Subject: Re: Size and release info for EMBL 39 Message-ID: <1994Aug23.153006.5298@comp.bioz.unibas.ch> Organization: EMBnet Switzerland [Basel] X-Newsreader: TIN [version 1.2 PL2] References: <1994Aug23.142956.18693@nomina.lu.se> Date: Tue, 23 Aug 1994 15:30:06 GMT Lines: 91 Bo Servenius (Bo.Servenius@wblab.lu.se) wrote: : Could ylu please point me to info about the size and releasedate of EMBL v39. As always, it is on bioftp.unibas.ch in one of the root menu items: EMBnet BioInformation Resource (Switzerland) 1. About Gopher, and this bioftp site/ 2. Biology subject tree in Gopher/ 3. DIBUG [Discover Insight Biosym User Group] Mailing list/ --> 4. EMBNet BioInformation Resource Switzerland/ 5. GCG Software Manual/ 6. Infoservers in European Countries/ 7. and if you have suggestions or problems.... [ 7Jan94, 1kb]. 8. development site of GOPHER (U Minnesota)/ 9. selected USENET News/ 1. About EMBnet/ --> 2. Database/ 3. Hints/ 4. Info on this EMBNet Information Resource [ 7Jan94, 4kb]. 5. Other EMBnet Hosts and Sources of Information/ 6. Software/ 1. About these searches [18Jan94, 1kb]. --> 2. EMBL/ 3. EMBL updates/ 4. Experimental/ 5. GENBANK (Indiana)/ 6. Genomes/ 7. More DNA searches/ 8. Protein databases (NIH)/ 9. general database searches (HOPKINS)/ --> 1. Release Notes [27Jun94, 22kb]. 2. Search in all EMBL data (last release on CD) Excerpts: EMBL Data Library Nucleotide Sequence Database Release Notes Release 39, June 1994 ... The EMBL nucleotide sequence database was frozen to make Release 39 on 6th June1994. The release contains 182,615 sequence entries comprising 192,195,819nucleotides. This represents an increase of about 8% over Release 38. Thesefigures do not include data in the file which contains patent data which havenot yet been fully integrated into the database. A breakdown of Release 39 bytaxonomic division is shown below: Division Entries Nucleotides ----------------- ------- ------------ Bacteriophage 991 1343992 ESTs 35353 11177758 Fungi 6639 13114445 Invertebrates 11705 20310436 Organelles 6071 7682925 Other Mammals 5138 6027529 Other Vertebrates 5931 6924533 Plants 9030 11350492 Primates 29014 30287388 Prokaryotes 17640 30484972 Rodents 20793 23422518 STSs 5346 1626193 Synthetic 6463 3317705 Unclassified 5429 3650188 Viruses 17072 21474745 ----------------- ------- ------------ Total 182615 192195819 plus: Other patents 3268 951445 ----------------- ------- ------------ Grand Total 185883 193147264 regards Reinhard -- +---------------------------+-------------------------------------------+ | Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 | | Biocomputing | electronic Mail doelz@urz.unibas.ch | |Biozentrum der Universitaet+-------------------------------------------+ From owner-embldatabank@net.bio.net Tue Aug 23 23:00:00 1994 Path: biosci!bcm!gazette.bcm.tmc.edu!rsmith From: rsmith@dot.bcm.tmc.edu (Randall Smith) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Subject: BCM Sequence Annotation Web Server Date: 24 Aug 1994 11:14:20 GMT Organization: Institute for Molecular Genetics, Baylor College of Medicine Lines: 64 Distribution: world Message-ID: NNTP-Posting-Host: dot.imgen.bcm.tmc.edu Xref: biosci bionet.molbio.genbank:1717 bionet.molbio.embldatabank:357 bionet.molbio.genome-program:911 bionet.molbio.proteins:2518 Announcing a new WWW Server: The BCM Sequence Annotation Server URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html Developed by Kanwal Gill, Brent Wiese, and Randall Smith Human Genome Center, Baylor College of Medicine, Houston TX USA We have created a "Sequence Annotation" WWW Server that allows researchers to add their own annotations to Entrez (NCBI) DNA and protein sequence reports. Our Annotation Server is intended as a method for investigators to easily share new information about sequences, e.g., new features, interesting sequence matches, domain identifications, etc. A user who wishes to make an annotation for an Entrez sequence will be given the chance to select an annotation type (eg coding region, variant, etc.). The user is then requested to enter a short annotation that will appear as an embedded link in an Entrez report. The annotator will then be prompted to enter an extended commentary which gives the further details about the annotation. The annotator may also enter some keywords that can be searched on and URL's that will lead to more information (eg, an entry in another database, a file of data on the annotator's home computer, etc). Only the annotations themselves are stored on our local server. When a user wishes to view an annotated record, our server requests a sequence report from the NCBI Entrez Server. The local annotations are then embedded within the returned report. As an initial entry, we have added several hundred annotations based on data kindly provided by Keith Robison. The annotations list probable coding regions within bacterial sequences that are not annotated as such in GenBank (see Table 2 of K. Robison, W. Gilbert and G.M. Church, "Large scale bacterial gene discovery by similarity search", Nature Genetics 7:205, 1994). We invite the biological community to use the server to view this data as well as to add data of their own. Users wishing to view the data need only the URL listed above and a graphical WWW browser such as Mosaic or Chimera. Users wishing to add data would be well-advised to also prepare the text of their annotation and extended commentary as well as to have their URL's (if any) in mind before beginning. Extensive on-line help is provided for both types of users. Suggestions and comments regarding how the server can best meet the needs of the biological community are welcome. There is a comments form provided in the server for typing in your comments. Comments may also be emailed to Randall Smith at rsmith@bcm.tmc.edu. ------------------------------------------------------------------------ Randall F. Smith Human Genome Center Department of Molecular and Human Genetics and W.M. Keck Center for Computational Biology Baylor College of Medicine Houston, TX 77030 USA rsmith@bcm.tmc.edu 713-798-4735; FAX: 713-798-5386 ------------------------------------------------------------------------ From owner-embldatabank@net.bio.net Tue Aug 23 23:00:00 1994 Path: biosci!biosci!not-for-mail From: rsmith@DOT.IMGEN.BCM.TMC.EDU (Randall Smith) Newsgroups: bionet.announce,bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Subject: BCM Sequence Annotation Web Server Date: 24 Aug 1994 12:54:21 -0700 Organization: Institute for Molecular Genetics, Baylor College of Medicine Lines: 63 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.announce:1371 bionet.molbio.genbank:1721 bionet.molbio.embldatabank:358 bionet.molbio.genome-program:912 bionet.molbio.proteins:2523 Announcing a new WWW Server: The BCM Sequence Annotation Server URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html Developed by Kanwal Gill, Brent Wiese, and Randall Smith Human Genome Center, Baylor College of Medicine, Houston TX USA We have created a "Sequence Annotation" WWW Server that allows researchers to add their own annotations to Entrez (NCBI) DNA and protein sequence reports. Our Annotation Server is intended as a method for investigators to easily share new information about sequences, e.g., new features, interesting sequence matches, domain identifications, etc. A user who wishes to make an annotation for an Entrez sequence will be given the chance to select an annotation type (eg coding region, variant, etc.). The user is then requested to enter a short annotation that will appear as an embedded link in an Entrez report. The annotator will then be prompted to enter an extended commentary which gives the further details about the annotation. The annotator may also enter some keywords that can be searched on and URL's that will lead to more information (eg, an entry in another database, a file of data on the annotator's home computer, etc). Only the annotations themselves are stored on our local server. When a user wishes to view an annotated record, our server requests a sequence report from the NCBI Entrez Server. The local annotations are then embedded within the returned report. As an initial entry, we have added several hundred annotations based on data kindly provided by Keith Robison. The annotations list probable coding regions within bacterial sequences that are not annotated as such in GenBank (see Table 2 of K. Robison, W. Gilbert and G.M. Church, "Large scale bacterial gene discovery by similarity search", Nature Genetics 7:205, 1994). We invite the biological community to use the server to view this data as well as to add data of their own. Users wishing to view the data need only the URL listed above and a graphical WWW browser such as Mosaic or Chimera. Users wishing to add data would be well-advised to also prepare the text of their annotation and extended commentary as well as to have their URL's (if any) in mind before beginning. Extensive on-line help is provided for both types of users. Suggestions and comments regarding how the server can best meet the needs of the biological community are welcome. There is a comments form provided in the server for typing in your comments. Comments may also be emailed to Randall Smith at rsmith@bcm.tmc.edu. ------------------------------------------------------------------------ Randall F. Smith Human Genome Center Department of Molecular and Human Genetics and W.M. Keck Center for Computational Biology Baylor College of Medicine Houston, TX 77030 USA rsmith@bcm.tmc.edu 713-798-4735; FAX: 713-798-5386 ------------------------------------------------------------------------ From owner-embldatabank@net.bio.net Mon Aug 29 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!sun4nl!news.nic.surfnet.nl!news.wau.nl!VLINDERS@rcl.wau.nl From: vlinders@rcl.wau.nl (Meindert de Jong) Newsgroups: bionet.molbio.embldatabank Subject: Invitation for an Academic Promotion Date: 30 Aug 1994 09:17:56 GMT Organization: Wageningen Agricultural University Lines: 20 Message-ID: <33utg4$4j7@trex.iend.wau.nl> Reply-To: vlinders@rcl.wau.nl NNTP-Posting-Host: rvd.wau.nl I just received the PhD Thesis of Dion Florack entitled: "Application of Hordothionins and Cecropin B for Engineering Bacterial Disease Resistance into Plants" Keywords: biotechnology, genetic engineering, breeding for bacterial disease resistance; He will defend his Thesis on September 21 4:00 pm at the Auditorium of Wageningen Agricultural University. The promotion will be followed by a reception. A party will be held in the evening. You are cordially invited to join the graduation. Dion's transgenic plants of tobacco and tomato will be exten- sively tested for field resistance against Xanthomas campes- tris pv. vesicatoria by the University of Florida. Dion's business address: Centre for Plant Breeding and Reproduction Research (CPO-DLO) P.O.Box 16 6700 AA Wageningen Netherlands {Meindert de Jong AKA Vlinders@rcl.wau.NL} From owner-embldatabank@net.bio.net Tue Aug 30 23:00:00 1994 Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Path: biosci!galaxy.ucr.edu!ihnp4.ucsd.edu!library.ucla.edu!agate!dog.ee.lbl.gov!news.cs.utah.edu!emba-news.uvm.edu!brianf From: brianf@med.uvm.edu (Brian Foley) Subject: Re: BCM Sequence Annotation Web Server Message-ID: <1994Aug31.142529.4040@emba.uvm.edu> Followup-To: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Sender: news@emba.uvm.edu Organization: EMBA Computer Facility, University of Vermont X-Newsreader: TIN [version 1.2 PL1] References: Date: Wed, 31 Aug 1994 14:25:29 GMT Lines: 29 Xref: biosci bionet.molbio.genbank:1728 bionet.molbio.embldatabank:360 bionet.molbio.genome-program:921 bionet.molbio.proteins:2562 Randall Smith (rsmith@dot.bcm.tmc.edu) wrote: : Announcing a new WWW Server: The BCM Sequence Annotation Server : URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html : Developed by Kanwal Gill, Brent Wiese, and Randall Smith : Human Genome Center, Baylor College of Medicine, Houston TX USA : We have created a "Sequence Annotation" WWW Server that allows : researchers to add their own annotations to Entrez (NCBI) DNA and : protein sequence reports. Our Annotation Server is intended as a : ... deletion to save bandwidth... This server appears to require a "forms-based" WWW CLient. A "forms-based" client has been available for UNIX systems for a while. A forms-based client for the Mac was recently released as well. It can be obtained from Info-Mac at Sumex-Aim via FTP it is called Mac-Web and the version there last night was 1.00a. It works great on my LCIII with only 4Mb or RAM. The annotation server above seemed to be down, but I tried it out on the Genome Database and it worked fine. -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldn't be called research * * University of Vermont * * ******************************************************************** From owner-embldatabank@net.bio.net Wed Aug 31 23:00:00 1994 Path: biosci!CS.Arizona.EDU!uunet!cs.utexas.edu!howland.reston.ans.net!wupost!bcm!gazette.bcm.tmc.edu!rsmith From: rsmith@dot.bcm.tmc.edu (Randall Smith) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Subject: Re: BCM Sequence Annotation Web Server Followup-To: bionet.molbio.genbank,bionet.molbio.embldatabank,bionet.molbio.genome-program,bionet.molbio.proteins Date: 01 Sep 1994 01:45:29 GMT Organization: Institute for Molecular Genetics, Baylor College of Medicine Lines: 46 Distribution: world Message-ID: References: <1994Aug31.142529.4040@emba.uvm.edu> NNTP-Posting-Host: dot.imgen.bcm.tmc.edu In-reply-to: brianf@med.uvm.edu's message of Wed, 31 Aug 1994 14:25:29 GMT Xref: biosci bionet.molbio.genbank:1731 bionet.molbio.embldatabank:361 bionet.molbio.genome-program:923 bionet.molbio.proteins:2572 Brian Foley (brianf@med.uvm.edu's message of Wed, 31 Aug 1994 14:25:29 GMT) wrote: >Randall Smith (rsmith@dot.bcm.tmc.edu) wrote: > >: Announcing a new WWW Server: The BCM Sequence Annotation Server >: >: URL: http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html >... > > This server appears to require a "forms-based" WWW CLient. >A "forms-based" client has been available for UNIX systems for >a while. A forms-based client for the Mac was recently released >as well. It can be obtained from Info-Mac at Sumex-Aim via FTP >it is called Mac-Web and the version there last night was >1.00a. It works great on my LCIII with only 4Mb or RAM. A forms-based WWW client is needed. However, Mac Mosaic 2.0a6 *is* now available from NCSA -- I have it running on my Mac and the forms work fine. See: http://www.ncsa.uiuc.edu/SDG/Software/MacMosaic/MacMosaicHome.html >The annotation server above seemed to be down, but I tried it out on >the Genome Database and it worked fine. Our system disk crashed Mon. afternoon and our machine has been down. It's up now. Please try the server out and let us know what you think. -Randall Smith ------------------------------------------------------------------------ Randall F. Smith Human Genome Center Department of Molecular and Human Genetics and W.M. Keck Center for Computational Biology Baylor College of Medicine Houston, TX 77030 USA rsmith@bcm.tmc.edu 713-798-4735; FAX: 713-798-5386 ------------------------------------------------------------------------