From owner-embldatabank@net.bio.net Thu Jun 01 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!lhc!borduas!francis From: francis@borduas.nlm.nih.gov (Francis Ouellette) Subject: Re: DNA sequence of pGFP Message-ID: <1995Jun2.064610.12650@nlm.nih.gov> Sender: news@nlm.nih.gov Organization: National Library of Medicine X-Newsreader: TIN [version 1.2 PL2] References: <3qjug5$3st@stud.Direct.CA> Date: Fri, 2 Jun 95 06:46:10 GMT Lines: 32 Akio Abe (akioabe@portal.ca) wrote: > I am looking for a sequence data of plasmid pGFP, encoding green > fluorescence gene. > Please let me know the FTP site of sequence data or any information. > I am look forward to hearing soon from you. dear AKIO if you use the retrieve server at GenBank/NCBI or the netserv at EMBL/EBI you should be able to find the sequence you want. The accession number is U19276. here is part of the file: > LOCUS XXU19276 4146 bp DNA circular SYN 24-MAY-1995 > DEFINITION Cloning vector pGFP-1 green fluorescent protein, complete cds. > ACCESSION U19276 To Obtain Help Documentation: send e-mail to 'retrieve@ncbi.nlm.nih.gov' with the word 'help' in the body of the mail message. Send the same message to: netserv@ebi.ac.uk to get info on how to use the EMBL/EBI server. regards, francis -- | B.F. Francis Ouellette | | francis@ncbi.nlm.nih.gov From owner-embldatabank@net.bio.net Tue Jun 06 23:00:00 1995 Path: biosci!bloom-beacon.mit.edu!usc!news.cerf.net!newsserver.sdsc.edu!news.tc.cornell.edu!travelers.mail.cornell.edu!newsstand.cit.cornell.edu!NewsWatcher!user From: pts3@cornell.edu (phil) Newsgroups: bionet.molbio.embldatabank Subject: Help!! Paper Wasps Needed Followup-To: bionet.molbio.embldatabank Date: 7 Jun 1995 02:48:46 GMT Organization: cornell Lines: 24 Sender: pts3@cornell.edu (Verified) Message-ID: NNTP-Posting-Host: cu-dialup-0615.cit.cornell.edu Hello. My name is Phil Starks. I am a graduate student at Cornell University in the field of NeuroBiology and Behavior. I am currently examining paper wasps, specifically Polistes dominulus. I am evaluating their nesting behavior and population genetics. I want to compare animals from different regions -- mostly from the Northeast in areas between Boston, MA and Ithaca, NY. My problem is finding these critters. They tend to congregate in the eves of man-made structures. I have searched state parks and some universities but have only found 4 usable sites. A usable site is one that has been relatively undisturbed (not sprayed with insecticides) for a few years and contains 18 or more colonies. These wasps make un-enveloped nests -- you can plainly see the cells of the comb (it looks much like a gray honeycomb). P. dominulus is the more yellow and smaller of the 2 Polistes species in this region (P. fuscatus is dark brown and the larger of the two animals). At this time of year you may see colonies with anywhere from 1 to 10 individuals, and nests that may contain 8 to 100 cells. If you know of any potential sites please email me. I am offering a $20.00 finder fee for useful sites. Thanks for reading this message Phil Starks (pts3@cornell.edu) From owner-embldatabank@net.bio.net Tue Jun 06 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!bloom-beacon.mit.edu!usc!elroy.jpl.nasa.gov!swrinde!howland.reston.ans.net!news.sprintlink.net!uunet!in1.uu.net!sangam!iitb!powai!sndatta From: sndatta@powai.cc.iitb.ernet.in (prof s n datta) Subject: info on cytochrome f Message-ID: Date: Tue, 6 Jun 1995 10:05:52 GMT Organization: Computer Centre, Indian Institute of Technology, Bombay X-Newsreader: TIN [version 1.2 PL2] Lines: 6 dear netters, could someone tell me if the crystal structure of cytochrome f is available in the protein data bank. thanks in advance mallik From owner-embldatabank@net.bio.net Tue Jun 06 23:00:00 1995 Newsgroups: ebi.announce,ebi.servers,bionet.molbio.embldatabank,bionet.software Path: biosci!agate!howland.reston.ans.net!news.sprintlink.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: Changes to EBI-FTP database directories Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Wed, 7 Jun 1995 13:28:03 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 48 Xref: biosci bionet.molbio.embldatabank:514 bionet.software:12297 ********************************************************************** Between June 16th & 19th 1995, the subdirectories of /pub/databases/protein_extras/ will be reorganized on ftp.ebi.ac.uk (ftp.embl-ebi.ac.uk) ********************************************************************** On June 16th, a new entry will be created for all subdirectories that are currently located in /pub/databases/protein_extras/ These new directories will be located one level higher in the directory tree e.g. /pub/databases/protein_extras/hssp will become /pub/databases/hssp On June 19th, the old locations in /pub/databases/protein_extras/ will dissappear If you run a mirror process on any of the following directories then change your scripts during the period 16-19 June Affected directories: /pub/databases/protein_extras/dssp /pub/databases/protein_extras/fssp /pub/databases/protein_extras/ftphelp.txt /pub/databases/protein_extras/hssp /pub/databases/protein_extras/misfolded /pub/databases/protein_extras/models /pub/databases/protein_extras/nrl3d /pub/databases/protein_extras/pdb /pub/databases/protein_extras/pdb_select /pub/databases/protein_extras/puu /pub/databases/protein_extras/ras If you need more information, contact nethelp@ebi.ac.uk Jeroen -- ============================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ============================================================== From owner-embldatabank@net.bio.net Wed Jun 07 23:00:00 1995 Path: biosci!rutgers!gatech!howland.reston.ans.net!Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.rhrz.uni-bonn.de!ibm.rhrz.uni-bonn.de!UNC802 From: UNC802@ibm.rhrz.uni-bonn.de (Michael Breuer) Newsgroups: bionet.molbio.embldatabank Subject: DAHP-Synthase from plants Date: Thu, 08 Jun 95 16:52:00 MEZ Organization: RHRZ Uni-Bonn Lines: 12 Message-ID: <173B7ED30S85.UNC802@ibm.rhrz.uni-bonn.de> NNTP-Posting-Host: ibm.rhrz.uni-bonn.de Keywords: DAHP-Synthase, PCR, exons-introns Hello netters, in our group we are interested to clone the deoxy-arabino-heptulosonate- 7-phosphate synthase from plants of the Celastraceae family. We plan to amplify parts of the gene by PCR. Does anybody have some ideas about the location of exons/introns in the DAHP-synthase genes cloned from plants? All data I have at hand, stem from cDNA clones of the gene. Since we are notyet interested in the whole gene(s), we shyed away from the preparation of cDNA. Any help concerning the topic is appreciated. Cheers, Michael Breuer (unc802@ibm.rhrz.uni-bonn.de) From owner-embldatabank@net.bio.net Sun Jun 11 23:00:00 1995 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.embldatabank Subject: UNSUBSCRIBING, BIOSCI ARCHIVES, ADDRESS DATABASE & BIOSCI FAQ Date: 12 Jun 1995 02:02:44 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 347 Sender: daemon@net.bio.net Distribution: world Message-ID: <199506120900.CAA20406@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 on how to subscribe/unsubscribe 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 Mosaic or another World Wide Web browser and connect to the BIOSCI WWW home page at URL http://www.bio.net/. Select the hypertext link to the BIOSCI archives. This gives you read access to all newsgroup messages and the ability to search the indexes described below. You can also 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 fix problems that you might encounter in using the newsgroups. The FAQ and other BIOSCI documentation is available through our WWW home page at URL http://www.bio.net/. It is also 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, gopher, and WWW access (the URL is http://www.bio.net). 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: > > --> 14. 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. > > > 6. Information in English/ > > 5. Scientific and other topics/ > > 1. Finnish EMBnet BioBox/ > > 9. FAQ Files/ > > 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 ASCB bionet.prof-society.ascb BIOCAN bionet.prof-society.cfbs 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 BIO-WWW bionet.software.www CARDIOVASCULAR-RESEARCH bionet.biology.cardiovascular CELEGANS bionet.celegans CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CSM bionet.prof-society.csm CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMF-BIO bionet.emf-bio EMPLOYMENT bionet.jobs EMPLOYMENT-WANTED bionet.jobs.wanted FASEB bionet.prof-society.faseb 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 MICROBIOLOGY bionet.microbiology MOLECULAR-EVOLUTION bionet.molbio.evolution MOLECULAR-MODELLING bionet.molec-model MOLLUSC-MOLECULAR-NEWS bionet.molbio.molluscs 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 STADEN bionet.software.staden STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical URODELES bionet.organisms.urodeles VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeast ZBRAFISH bionet.organisms.zebrafish 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 Jun 15 23:00:00 1995 Newsgroups: bionet.molbio.embldatabank Path: biosci!rutgers!uwm.edu!cs.utexas.edu!news.sprintlink.net!pipex!lyra.csx.cam.ac.uk!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!bshomer From: bshomer@ebi.ac.uk (Benny Shomer) Subject: EMBL WWW sequence submissions - FAQ list. Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Fri, 16 Jun 1995 12:48:39 GMT Organization: EBI - European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 415 EMBL nucleotide sequences database WWW sequence submission system The FAQ list %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This is the first version of the WWW based sequence data submission tool Frequently Asked Questions (FAQ) list. The FAQ list has been produced taking into consideration various queries and problems that scientists from the users community have experienced. It is probably far from being complete. We welcome any suggestions, questions highlights... Just send us mail at: datalib@ebi.ac.uk An HTML version of the FAQ file can be found on: http://www.ebi.ac.uk/subs/subs_faq.html or linked to, from the submission system page in the EMBL area of EBI home page at: http://www.ebi.ac.uk/ 1. What are the advantages of using EBI's WWW based sequence submission tool? 2. Will my sequence be processed faster than normal when I use the WWW based system? How soon will I get my accession number? 3. I need my accession number as soon as possible. Any guidelines? 4. Can I submit protein sequences with this tool? 5. Which platforms / browsers are compatible with the system? 6. Why is the submission system divided into so many parts? 7. I have a few sequences - do I need to type all the information time and time again? 8. I have previously submitted a sequence to EMBL. Can some of my data be used again for this submission? 9. I specified my previous accession number but the system could not locate my entry. What's going on here?... 10. What's this thing with freezing a submission? How do I do it? 11. Is there a length limit for the sequence? why? 12. Must I specify features for the sequence? 13. Can I copy & paste my sequence with numbers etc.? 14. My system / browser has crashed. What do I do?... 15. I forgot to write my unique Id. How do I get it? 16. Why is it so important not to step back? When is it needed? 17. How can I add a feature from the final validation form? 18. How can I remove a feature from the final validation form? 19. During submission of the features I went into an endless loop, why did this happend? How do I get out of it? 20. How do I request further help? 21. I have finished all my submissions, how do I stop the program? ================================================================== 1. What are the advantages of using EBI's WWW based sequence submission tool? a. In contrast to a stand-alone program, EBI constantly maintains and updates the program. This makes debugging and keeping up-to-date a lot easier. b. If you already have the WWW client installed, you don't have to waste time, effort and disk space on installation of a program on your computer. c. The program uses the EBI database resources (like the list of previous submitters, or journals), to enable a more user-friendly interface. d. You may freeze your session for a very long time. e. You can tell your friends that you have submitted a sequence using EBI's new system... +++ 2. Will my sequence be processed faster than normal when I use the WWW based system? How soon will I get my accession number? Generally, the process of submission is made somewhat shorter, since the submission system itself, prevents the user from many common mistakes during submission (like leaving out mandatory items, detecting minor errors etc). The system also enables EBI's data annotation staff to automate the processes of loading the submitter's personal details and the sequence data into the database system. Since your data comes in already formated in the most optimal way for us to process, it saves some manual editing steps. We will process data submissions within 24-48 hours of receipt and send authors notification of either what accession number(s) their data have been assigned or what additional information is needed. +++ 3. I need my accession number as soon as possible. Any guidelines? There are several things authors can do to minimize the time it takes to get an accession number: a. Be sure that submissions include all the necessary information and that all relevant questions have been fully answered. A very common trap for many users is not providing the sequence features. This introduced a delay, since our data annotators must communicate with the submitter, asking for that information. b. Check the data to be sure that they do not contain inconsistencies / errors (e.g., a stop codon in the middle of a coding region). c. Take extra care and check that the provided Email address is accurate. The submission system checks some syntax rules and the country domain provided, but can't do more than that. If a wrong Email address is provided, any attempt for further communication will slowed down the process. Your precise phone and fax number will also help. +++ 4. Can I submit protein sequences with this tool? The submission system is currently intended, and is specifically designed for submission of nucleotide sequences only. If you need to submit protein sequences to SWISS-PROT, please send a request for a data submission form to: datalib@ebi.ac.uk +++ 5. Which platforms / browsers are compatible with the system? The submission system has been thoroughly tested and is known to be compatible with all the common platforms (i.e. PC's Mac's Xclients and workstations). Most of the common browsers have been tested: mosaic, Netscape, MacWeb, lynx, Magimix. Users of Netscape for Mac & PC's should be aware of a Netscape acossiated limitations. Some Netscape browsers are incapable of saving the html source code generated by scripts (in fact they simply do it in the wrong way, asking the server to reload the source, something a CGI script can not provide). Users of Netscape should not attempt to 'freeze' their submission (see section 9), by saving the HTML source code of the form. They should resume their session by using the rescue mechanism provided by the system (see section 12). +++ 6. Why is the submission system divided into so many parts? The task of submitting a sequence to the databank(s) is a very complicated and demanding one. Breaking the process to many smaller forms enables some major advantages: a. It enables a high level of interactivity with the user. The system responds on the users input, checking validity on many data fields. b. It enables data hiding. Data items which are of no concern to all the users will be hidden and will appear only when the need arises. For example, if you submit a human cDNA, you don't need to see questions related to viral sequences. c. It enables managing the complicated task even when the network load is heavy. The forms are broken into a single network packet (or two), so traffic is cut down to a minimum. +++ 7. I have a few sequences - do I need to type all the information time and time again? Having X different sequences, calls for cycling through the submission system X times. Yet, the system will keep most of the submission details (according to your specifications) for re-usage. This means that on each of the remaining X-1 submissions, the selected forms will appear pre-filled with the appropriate details. The chance to specify which details should be recycled by the system is given following the completion of each submission. If you intend to submit several sequences that are related to each other, please mention this in the first page of the submission system, so that our sequence annotation group will know to process them together. +++ 8. I have previously submitted a sequence to EMBL. Can some of my data be used again for this submission? Yes. If your submission has been made directly to EMBL / EBI you may type your previous accession number. That will get you the first form of your personal details pre-filled with your details as they appear in the database. You have an option to modify any details if needed. Please review your data and check for any errors. +++ 9. I specified my previous accession number but the system could not locate my entry. What's going on here?... Well, normally - either your entry is still tagged as confidential, so it's not available to the public, or it is new and is not yet updated in the local names database of the submission system (it is not an automatic process yet). If neither is true, please let us know about it. It will be checked. +++ 10. What's this thing with freezing a submission? How do I do it? Before your submission is complete your data items are stored in a temporary storage area and are identified by your unique Id. Each one of the submission forms is carrying the unique Id in the HTML source code. When you submit the form, the system picks up the unique Id and acts accordingly. This means that if you will save the HTML source code to your disk, and open it later on as a local file, you will be able to press continue and go on with the submission. This is true for the amount of time specified by EBI (currently unlimited). To freeze - From the file menu, choose "save as..." and specify "HTML" or "source" (according to the type of browser). Be sure to provide a name that ends with .html (or .htm for PC's). When you want to resume the submission process, choose from the "file" menu, "open local" or "open file" (again, according to the type of browser) and specify your saved document. Fill it in, press 'continue' and watch the submission process comes back to life... Alternatively (and maybe even preferred...), you can use the rescue mechanism to renew a stopped session. See the explanations in section 14. Freezing enables you to gather pieces of information you have forgotten, go get coffee from the coffee machine, fall asleep leaning on your monitor or take a plane to Hawaii (unless your'e lucky enough to be there already), leaving us in anticipation :-) Users of Netscape - be aware of some limitations. See section 4. +++ 11. Is there a length limit for the sequence? why? Due to a current limitation of the WWW system, there is no possibility to transfer documents larger than 22500 characters. This means you can not submit directly, sequences larger than 22500 base pair. What to do if your sequence is longer than that? Instead of a real sequence, type in 4 bases, and send (only) the sequence itself to datasubs@ebi.ac.uk mentioning your unique Id. If you know in advance about this (you obviously do if you are reading this FAQ list...), please mention this fact in the comments box at the begining (or end) of the submission process. +++ 12. Must I specify features for the sequence? Indeed so. If you fail to provide the appropriate features, it will cause delays in the processing of your entry (See section 6). This is, since the data annotators will have to communicate with you further, to obtain the features from you. +++ 13. Can I copy & paste my sequence with numbers etc.? If you copy and paste your sequence from any program or text editor, the sequence may contain spaces, tabs and numbers. These will not be regarded by the system and your sequence will be reformated. +++ 14. My system / browser has crashed. What do I do?... Ouch. It's time for a rescue... From the submission home page (the one with the logo), there's a link to a "crash proof system". Select this link, specify the unique Id that is given to you at the begining of the submission and pray. You will be taken to the last step at which your submission has stopped. This however, refers to a submission while it is at process. After the submission has been completed, the rescue mechanism can not be in operation. You may certainly use the rescue mechanism instead of "freezing" your submission at any time (although molecular biologists DO tend to freeze everything...). +++ 15. I forgot to write my unique Id. How do I get it? Just send a request by email to: datalib@ebi.ac.uk We can detect your unique Id, provided your entry still exists in the system. +++ 16. Why is it so important not to step back? When is it needed? On any step of the submission, if you go back to more than one previous form and press "continue", it will result in loss of the recent data items. Say that you have submitted 1, 2, 3, 4 and 5. You now press 'back' and go to 3, then you press "continue", it will erase 4 and 5. If, however, you step only one form back and press "continue", your data is safe. This allows you to correct the last form you entered. So what if I'm at step 5 and discovered an error in 2? There is a special form at the end, allowing you to correct any data item you wish. Please use it. +++ 17. How can I add a feature from the final validation form? If you need to add a feature during the final validation step (where you are given the full list of all your data for approval), select the last feature's checkbox (that is unless you need to correct a feature entry anyway), and continue. Continue (unless a correction is needed) without change. You will get back to the final validation step, but two empty feature entries will be appended to the list. Check one of their boxes and press "continue", to enter their data. Specific help for each feature's options and qualifiers is given after selecting a feature. If you have initially chosen not to add any feature, but made up your mind to add one in the final validation step, check the box for correcting the sequence and press continue after specifying that you need a feature. Again - you will have a checkbox associated with an empty area. Check it and press continue. +++ 18. How can I remove a feature from the final validation form? Check the feature's checkbox and press continue. This will give you a chance to correct the feature's entry. Specify locations from 0 to 0, leaving the qualifiers lists empty. This is a sign for us to cancel this feature entry. DO NOT leave both feature lists empty (i.e. containing '------'). This will get you into an endless loop with funny looking qualifier boxes. If you have mistakenly went into such a loop, simply step back, and re-submit the unwanted feature as described above. +++ 19. During submission of the features I went into an endless loop, why did this happend? How do I get out of it? The system currently enters an endless loop if both feature lists are left empty (i.e. containing '------'). If you have mistakenly went into such a loop, simply step back, and re-submit with a feature selected. If it happend while trying to cancel a previously submitted feature, see section 18. +++ 20. How do I request further help? Open the window and shout "HELLLLP", or... In any of the submission's context sensitive help files, at the bottom, there's a special area where you can type your help request. Be sure to enter your correct Email address. You can also send Email directly to: datalib@ebi.ac.uk. Please specify your problem in clear words and try to be as descriptive as you can. +++ 21. I have finished all my submissions, how do I stop the program? There's actually nothing to stop. If you don't intend to submit any more sequences, just use your Web browser as you would normally. Either choose any other URL, go to EBI's home page, kill your browser... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Benny Shomer External Biological Liaison Officer, EMBL outstation - The EBI, Hinxton Hall, Hinxton,Cambridge CB10 1RQ, UK Tel: +44-223-494437 Fax: +44-223-494468 Email: bshomer@EBI.ac.uk http://www.ebi.ac.uk/ebi_docs/staff/benny.html ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-embldatabank@net.bio.net Wed Jun 21 23:00:00 1995 Newsgroups: ebi.servers,bionet.molbio.embldatabank,bionet.software,bionet.genome.arabidopsis,bionet.genome.chromosomes,bionet.molbio.genome-program,bionet.molbio.yeast,embnet.general Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!cam.news.pipex.net!pipex!edi.news.pipex.net!pipex!sunsite.doc.ic.ac.uk!hgmp.mrc.ac.uk!ebi.ac.uk!jecop From: jecop@ebi.ac.uk (Jeroen Coppieters) Subject: ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER Sender: news@ebi.ac.uk (Mr news) Message-ID: Date: Thu, 22 Jun 1995 13:33:53 GMT Organization: European Bioinformatics Institute X-Newsreader: TIN [version 1.2 PL2] Lines: 151 Xref: biosci bionet.molbio.embldatabank:519 bionet.software:12432 bionet.genome.arabidopsis:3455 bionet.genome.chromosomes:664 bionet.molbio.genome-program:1422 bionet.molbio.yeast:3158 ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER >From June 20th on, GeneMark will be reachable at the EMBL Outstation - The European Bioinformatics Institute (EBI), Hinxton, UK EMAIL: genemark@embl-ebi.ac.uk (or genemark@ebi.ac.uk) as well as on the original site School of Biology, Georgia Institute of Technology (Atlanta, GA) EMAIL: genemark@ford.gatech.edu Since its first announcement, the GeneMark program has undergone continuous improvements, and more species matrices are made available for usage with the service. The EMBL-EBI server is a mirror of the Georgia one, and thus will return the same results for the same queries. 1. SHORT OVERVIEW OF GENEMARK FEATURES --------------------------------------------- The GeneMark server provides e-mail based identification of protein coding regions in DNA sequences from prokaryotic and eukaryotic species. The GeneMark server accepts a formatted message containing a DNA sequence in text format. You may specify a species name, and parameters that control the analysis procedure. The current GeneMark version is accurate for finding prokaryotic genes and for analyzing cDNA sequences to discriminate coding regions from non-coding ones like 5' or 3' UTRs. This program is able to identify rather long exons (more than 100bp) in eukaryotic genomic DNA. This information can be used for designing RT-PCR or PCR primers. The GeneMark gene identification program has been developed at the School of Biology, Georgia Institute of Technology (Atlanta, GA). More details on the algorithm can be found in the paper: Borodovsky M. and McIninch J.D., GeneMark: Parallel gene recognition for both DNA strands, Computers & Chemistry, 1993, 17, 123-133. 2. SENDING DATA TO GENEMARK ----------------------------------------------------- A DNA sequence should be sent via e-mail to one of the following addresses: genemark@ford.gatech.edu or genemark@embl-ebi.ac.uk ... with the word 'genemark' in the 'Subject:' field There is only one mandatory keyword: DATA which must precede the text of the DNA sequence. Below is given a simple example of sending a sequence to the GeneMark server from a UNIX-based computer (note, that the '%' symbol is the prompt used by the system, and that lower-case letters in the sequence text, numbers and spaces are also acceptable): % mail genemark@embl-ebi.ac.uk (or % mail genemark@ford.gatech.edu) Subject: genemark data TCCAGCTACTGCTGCTAGCTACGCTAGTCG........ % When the server receives such a message, with almost no special options indicated, it will analyze the sequence using default options and send back a minimal response. Namely, it will use E. coli based parameters (by default) and send back to the submitter a message containing a list of those open reading frames that have been assessed as protein coding regions. You may, however, wish to get more information from the server. In that case, please retrieve the HELP-Message from the GeneMark server, which contains a full description of all commands and options 3. GETTING THE HELP MESSAGE FROM GENEMARK ------------------------------------------------ Send an e-mail with the word HELP in the 'Subject:' field to genemark@ford.gatech.edu or genemark@embl-ebi.ac.uk 4. THE LIST OF SPECIES THAT CAN BE ANALYZED USING GENEMARK ------------------------------------------------------------------------------ NOTE: The EMBL-EBI server supports retrieval of the current list of supported species. Send a message to genemark@embl-ebi.ac.uk with the command LIST ORG in the SUBJECT The matrix is specified using the 'SPECIES' command Use the line 'species ' anywhere before the line 'data' where is the name of one of the matrices listed below: Matrix Name Species ----------- -------------------------------------------------------------- arab Arabidopsis thaliana capri Mycoplasma capricolum (TGA = Trp) celegans Caenorhabditis elegans chicken Gallus gallus disco Dictyostelium discoideum ecoli Escherichia coli "native" genes [DEFAULT] ecophage Escherichia coli horizontally transferred genes euglena Euglena gracilis eugchlor Euglena gracilis chloroplasts frog Xenopus laevis fruitfly Drosophila melanogaster human Homo sapiens kpneu Klebsiella pneumoniae lacto Lactococcus species leprae Mycobacterium leprae mouse Mus musculus plasm Plasmodium falciparum rat Rattus norvegicus salm Salmonella typhimurium spombe Schizosaccharomyces pombe subt Bacillus subtilis tuberc Mycobacterium tuberculosis t4 Phage T4 urchin Lytechinus pictus yeast Saccharomyces cerevisiae -------------------------------------------------------------------------- -- ============================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ============================================================== From owner-embldatabank@net.bio.net Mon Jun 26 23:00:00 1995 Path: biosci!biosci!not-for-mail From: jecop@ebi.ac.uk (Jeroen Coppieters) Newsgroups: ebi.servers,bionet.molbio.embldatabank,bionet.software,bionet.genome.arabidopsis,bionet.genome.chromosomes,bionet.molbio.genome-program,bionet.molbio.yeast,embnet.general,bionet.announce Subject: ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER Date: 26 Jun 1995 18:21:19 -0700 Organization: European Bioinformatics Institute Lines: 151 Sender: biohelp@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Xref: biosci bionet.molbio.embldatabank:521 bionet.software:12475 bionet.genome.arabidopsis:3470 bionet.genome.chromosomes:668 bionet.molbio.genome-program:1428 bionet.molbio.yeast:3182 bionet.announce:2225 ANNOUNCEMENT OF EUROPEAN GENEMARK E-MAIL SERVER >From June 20th on, GeneMark will be reachable at the EMBL Outstation - The European Bioinformatics Institute (EBI), Hinxton, UK EMAIL: genemark@embl-ebi.ac.uk (or genemark@ebi.ac.uk) as well as on the original site School of Biology, Georgia Institute of Technology (Atlanta, GA) EMAIL: genemark@ford.gatech.edu Since its first announcement, the GeneMark program has undergone continuous improvements, and more species matrices are made available for usage with the service. The EMBL-EBI server is a mirror of the Georgia one, and thus will return the same results for the same queries. 1. SHORT OVERVIEW OF GENEMARK FEATURES --------------------------------------------- The GeneMark server provides e-mail based identification of protein coding regions in DNA sequences from prokaryotic and eukaryotic species. The GeneMark server accepts a formatted message containing a DNA sequence in text format. You may specify a species name, and parameters that control the analysis procedure. The current GeneMark version is accurate for finding prokaryotic genes and for analyzing cDNA sequences to discriminate coding regions from non-coding ones like 5' or 3' UTRs. This program is able to identify rather long exons (more than 100bp) in eukaryotic genomic DNA. This information can be used for designing RT-PCR or PCR primers. The GeneMark gene identification program has been developed at the School of Biology, Georgia Institute of Technology (Atlanta, GA). More details on the algorithm can be found in the paper: Borodovsky M. and McIninch J.D., GeneMark: Parallel gene recognition for both DNA strands, Computers & Chemistry, 1993, 17, 123-133. 2. SENDING DATA TO GENEMARK ----------------------------------------------------- A DNA sequence should be sent via e-mail to one of the following addresses: genemark@ford.gatech.edu or genemark@embl-ebi.ac.uk ... with the word 'genemark' in the 'Subject:' field There is only one mandatory keyword: DATA which must precede the text of the DNA sequence. Below is given a simple example of sending a sequence to the GeneMark server >From a UNIX-based computer (note, that the '%' symbol is the prompt used by the system, and that lower-case letters in the sequence text, numbers and spaces are also acceptable): % mail genemark@embl-ebi.ac.uk (or % mail genemark@ford.gatech.edu) Subject: genemark data TCCAGCTACTGCTGCTAGCTACGCTAGTCG........ % When the server receives such a message, with almost no special options indicated, it will analyze the sequence using default options and send back a minimal response. Namely, it will use E. coli based parameters (by default) and send back to the submitter a message containing a list of those open reading frames that have been assessed as protein coding regions. You may, however, wish to get more information from the server. In that case, please retrieve the HELP-Message from the GeneMark server, which contains a full description of all commands and options 3. GETTING THE HELP MESSAGE FROM GENEMARK ------------------------------------------------ Send an e-mail with the word HELP in the 'Subject:' field to genemark@ford.gatech.edu or genemark@embl-ebi.ac.uk 4. THE LIST OF SPECIES THAT CAN BE ANALYZED USING GENEMARK ------------------------------------------------------------------------------ NOTE: The EMBL-EBI server supports retrieval of the current list of supported species. Send a message to genemark@embl-ebi.ac.uk with the command LIST ORG in the SUBJECT The matrix is specified using the 'SPECIES' command Use the line 'species ' anywhere before the line 'data' where is the name of one of the matrices listed below: Matrix Name Species ----------- -------------------------------------------------------------- arab Arabidopsis thaliana capri Mycoplasma capricolum (TGA = Trp) celegans Caenorhabditis elegans chicken Gallus gallus disco Dictyostelium discoideum ecoli Escherichia coli "native" genes [DEFAULT] ecophage Escherichia coli horizontally transferred genes euglena Euglena gracilis eugchlor Euglena gracilis chloroplasts frog Xenopus laevis fruitfly Drosophila melanogaster human Homo sapiens kpneu Klebsiella pneumoniae lacto Lactococcus species leprae Mycobacterium leprae mouse Mus musculus plasm Plasmodium falciparum rat Rattus norvegicus salm Salmonella typhimurium spombe Schizosaccharomyces pombe subt Bacillus subtilis tuberc Mycobacterium tuberculosis t4 Phage T4 urchin Lytechinus pictus yeast Saccharomyces cerevisiae -------------------------------------------------------------------------- -- ============================================================== . O . Jeroen Coppieters . O O o O . Software Support O O O O *o O O Jeroen.Coppieters@embl-ebi.ac.uk O O O O( *o )O O (or jecop@ebi.ac.uk) )O O O O o* O O( ++44 1223 494422 O O O O( o* )O O )O O O O *o O O( EMBL Outstation EBI O O O O( *o )O O (European Bioinformatics Institute) )O @ O O o* O O( Hinxton Hall O O O( o* )O(' Hinxton ` O( *o O ' Cambridge CB10 1RQ ` O ' UK http://www.ebi.ac.uk ==============================================================