From owner-embldatabank@net.bio.net Fri Apr 02 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!gatech!concert!samba!wurzelma From: wurzelma@med.unc.edu (John Wurzelmann) Newsgroups: bionet.molbio.embldatabank Subject: DNA-Protein binding sites Message-ID: <1993Apr3.194357.26988@samba.oit.unc.edu> Date: 3 Apr 93 19:43:57 GMT Sender: usenet@samba.oit.unc.edu Organization: UNC-CH SOM General Clinical Research Center Lines: 18 Nntp-Posting-Host: gcrcslc1.med.unc.edu Newsgroups: bionet.molbio.genbank Subject: DNA sites which bind protein. Summary: Expires: Sender: Followup-To: Distribution: world Organization: UNC-CH SOM General Clinical Research Center Keywords: Doe anyone know of a database dedicated to DNA-Protein binding sites? We are interested in regulation of transcription. Please send E-mail if you know of such a database. Thanks. Thanks, John Wurzelmann (wurzelma@med.unc.edu) From owner-embldatabank@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!agate!howland.reston.ans.net!noc.near.net!uunet!nwnexus!immunex!farrah From: farrah@immunex.com (Terry Farrah) Newsgroups: bionet.molbio.embldatabank Subject: Re: sequence not available Message-ID: <1993Apr5.105558.58@immunex.com> Date: 5 Apr 93 18:55:58 GMT References: <9304011633.AA04460@temin.lanl.gov> Distribution: bionet Organization: Immunex Corporation, Seattle, WA Lines: 19 In response to questions about why database sequences are not always released immediately after publication, Paul Gilna comments (regarding GenBank): > ... we have conferred upon the submitting author, the > responsibility for updating and maintaining his or her data. This is sensible for every aspect of the data except publication status. When scientists ask that their data not be released prior to publication, it is often because they are in a competitive situation and are motivated to restrict access to their data. It is not surprising, then, that they don't make the effort to notify sequence databases when their data has been published. I like Renee Lippens' suggestion: > ... why not ask to the Journals or Publishers to notify the databanks when > a publication containing an Accession Number is issued. -- Terry Farrah (farrah@immunex.com) From owner-embldatabank@net.bio.net Sun Apr 04 23:00:00 1993 Path: biosci!TEMIN.LANL.GOV!pgil From: pgil@TEMIN.LANL.GOV (Paul Gilna) Newsgroups: bionet.molbio.embldatabank Subject: Re: sequence not available Message-ID: <9304052059.AA21544@temin.lanl.gov> Date: 5 Apr 93 20:59:02 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 84 Terry Farrah writes > In response to questions about why database sequences are not always > released immediately after publication, Paul Gilna comments > (regarding GenBank): > > ... we have conferred upon the submitting author, the > > responsibility for updating and maintaining his or her data. > > This is sensible for every aspect of the data except publication status. > When scientists ask that their data not be released prior to publication, > it is often because they are in a competitive situation and are motivated > to restrict access to their data. It is not surprising, then, that > they don't make the effort to notify sequence databases when their data > has been published. > > I like Renee Lippens' suggestion: > > ... why not ask to the Journals or Publishers to notify the databanks when > > a publication containing an Accession Number is issued. > > -- > Terry Farrah (farrah@immunex.com) > > Though with some journals it is stated more explicitly than with others (e.g., Cell), there is a form of agreement between the journal and the publishing scientist that expects that all data and reagents associated with the publication are to be shared with the scientific community. Deliberate delay in having the data released could be considered to be in ethical abbrogration of this understanding. But that is taking a stick to the problem. Let me give a simple example as to why it is in a scientist`s interests NOT to have the data held confidential. Except perhaps in a legal court of law, the act of submission has little bearing on whether a scientist has proprietary publishing rights (i.e., proof that group A got there first). On the other hand release of the data to the public domain has a very real bearing on these issues. nce out there, your data have associated with them, both a date of release and your name. Therefore the scientist who is worried about being scooped from competitive access can very easily be scooped by publication from those same competitors simply because his or her data were stuck in confidential status sitting around for a journal to get its publishing act together while the competitors data sailed gaily and publically by. I would suggest that given the rate and volume of data appearing in the public domain (approx 2 x 10**6 bp per week) today and the increasing acceptance of the databases as an electronic data publication forum, justification for confidential data by fear of competitor's access is becomming increasingly moot. Therefore it is more in one's interests to get the data out there than it is to hide them. This can certainly be evidenced by the fact that as a percentage of total submissions, we find that the fraction of confidential submissions is showing a definite downward trend. Finally, to bring into perspective that last point, much has been made in this issue of authors (or databases) inability to release confidential data in time to coincide with publication. Lest readers be left with the perception that all submittors are recalcitrant, let me reassure you that the trend is such as to suggest the exact opposite--more and more submittors are taking it upon themselves to inform us of changes to the publication status of their data (and much more besides)--many with our help!. Further, we find we are handling considerably less "I couldn't retrieve the following sequence" queries, which once represented the *only* class of messages coming to update when we started it. While we are by no means at 100% compliance, we are definitely headed in that direction. > > I like Renee Lippens' suggestion: > > ... why not ask to the Journals or Publishers to notify the databanks when > > a publication containing an Accession Number is issued. A number of journals, particularly Science, PNAS and Appl. Env. Micro. do this already for us, and we are grateful to them for that, yet increasingly the submitter is getting to us first. Cheers, --paul From owner-embldatabank@net.bio.net Mon Apr 05 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!pipex!uunet!haven.umd.edu!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.embldatabank Subject: Re: DNA-Protein binding sites Message-ID: <1993Apr5.155032.17913@welchgate.welch.jhu.edu> Date: 5 Apr 93 15:50:32 GMT References: <1993Apr3.194357.26988@samba.oit.unc.edu> Organization: Johns Hopkins Univ. Welch Medical Library Lines: 37 In article <1993Apr3.194357.26988@samba.oit.unc.edu> wurzelma@med.unc.edu (John Wurzelmann) writes: >Newsgroups: bionet.molbio.genbank > >Doe anyone know of a database dedicated to DNA-Protein binding sites? >We are interested in regulation of transcription. Please send E-mail if >you know of such a database. Thanks. > There are two databases which may be of interest to you - The Eukaryotic Promoter Database (EPD) and the Transcription Factor Database (TFD). You can search the EPD for keywords by gopher at merlot.welch.jhu.edu in the following directory: --> 12. Search Databases at Welchlab (Vectors, Promoters, NRL-3D, EST, OMI../ --> 3. EPD - Eukaryotic Promoter Database This site also has a link to a gopher search of TFD at NIH, look in the --> 3. Genbank, PIR, Swiss_PROT and other Database Searches/ directory and you'll see: --> 23. Search TFD You can ftp the entire databases from (among other places) ncbi.nlm.nih.gov in the /repository directory. You may also do a BLAST search of the DNA sequences in EPD via the NCBI mail server. Write me a note if you need help getting started with gopher or the mail server. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu From owner-embldatabank@net.bio.net Fri Apr 09 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: EMBL Release 34 Message-ID: <1993Apr10.221712.81239@embl-heidelberg.de> Date: 10 Apr 93 21:17:11 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 100 Release 34 of the EMBL Nucleotide Seqauence Database (March 1993) is being distributed on CD-ROM and magnetic tape. All CD's should now be on their way. I attach some extracts from the release notes concerning upcoming changes, namely: - new EST division, UNA becomes UNC (unclassified) - circular molecules to be indicated - sequence numbering introduced - feature table changes, new 'source' key replaces several others. Changes To Database Divisions Input from our user community indicates that a separation of "EST" data from the main data collection is advisable. In Release 35 in June 1993 we will introduce a new database division called EST to include all sequences marked by the keywords "expressed sequence tag" or "transcribed sequence fragment". These sequences are often determined by single-strand, single-read sequencing methods only and generally include no or only marginal annotation. The creation of the new EST division will enable users of our database to easily exclude this kind of data from their analyses, if so desired. The "Unclassified" division will be renamed from UNA to UNC to reflect the fact that it contains sequences which are not taxonomically classified. Molecule Topology As previously announced we will indicate molecules which are known to be circular by prefixing the molecule type on the ID line with the keyword "circular" as from Release 35 in June 1993. Please note that the absence of the keyword "circular" should *not* be taken to indicate that the molecule is definitely known not to be circular. An example of such a circular molecule's ID line is shown below: ID CLSPC1 standard; circular DNA; ROD; 346 BP. Sequence Numbering To aid reading the sequence bases in database entries, we will insert base numbers in columns 73-80 of each sequence line as from Release 35 in June 1993. The numbers will be right justified, and will indicate the number of the last base on each line. An example is shown below (the ruler is for your convenience and will not appear in the database entries): 1 10 20 30 40 50 60 70 80 +--------+---------+---------+---------+---------+---------+---------+---------+ SQ Sequence 245 BP; 60 A; 44 C; 77 G; 64 T; 0 other; agatcttctg ctcccaggag agagagcaat gtctagagta gggaaaagga ccatcttagc 60 cctctactat aggcagctgt ctgctacccg tcactcacca atgggagagg aggcatgggt 120 attgtgttca gatggggccc agtgttattt atttgagact ggatcagggt gagaacttga 180 ggggaagggt tggagtagaa ggttatgatc tttctagaca gtgctgcatt ggtggcttga 240 ctgac 245 // +--------+---------+---------+---------+---------+---------+---------+---------+ 1 10 20 30 40 50 60 70 80 Feature Table Changes The following changes to the common DDBJ/EMBL/GenBank feature table will be implemented on April 1st 1993 and will therefore be reflected at Release 35 in June 1993. They are more fully documented in a document "The DDBJ/EMBL/GenBank Feature Table: Definition" which is available either in printed form from the EMBL Data Library, or electronically as a compressed postscript file from our anonymous FTP server: FTP.EMBL-Heidelberg.DE (Internet address) /pub/databases/embl/doc/FTv1.04.ps.Z (file name) Discontinued feature keys (superceded by "source" key): provirus, cellular, transposon, insertion_seq. New feature keys: source identifies the biological source of the specified span of the sequence. STS Sequence Tagged Site V_segment variable segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta and gamma chains. D_segment diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain. J_segment joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta and gamma chains. S_region switch region of immunoglobulin heavy chains. N_region extra nucleotides inserted between rearranged immunoglobulin segments. C_region constant region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta and gamma chains. V_region variable region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta and gamma chains. From owner-embldatabank@net.bio.net Sun Apr 11 23:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.embldatabank Subject: BIOSCI/bionet Frequently Asked Questions Message-ID: <9304120900.AA20938@net.bio.net> Date: 12 Apr 93 09:00:02 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 16 New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-embldatabank@net.bio.net Tue Apr 20 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!zaphod.mps.ohio-state.edu!saimiri.primate.wisc.edu!caen!batcomputer!ghost.dsi.unimi.it!genes!pongor From: pongor@genes.icgeb.trieste.it (Sandor Pongor) Newsgroups: bionet.molbio.embldatabank Subject: ICGEB/EMBnet Practical Course: Computers in Molecular Biology Keywords: Computer course, Biocomputing, Sequence Databases Message-ID: <1993Apr21.143027.19292@genes.icgeb.trieste.it> Date: 21 Apr 93 14:30:27 GMT Organization: ICGEB Lines: 114 Practical Course "Computer Methods in Molecular Biology" International Centre for Genetic Engineering and Biotechnology 14-23 July 1993, Trieste-Italy Co-sponsored by ICGEB and EMBnet/BRIDGE Organizer: Sandor Pongor, ICGEB Trieste, Italy Faculty: Amos Bairoch, University of Geneva, Geneva, Switzerland Dennis Benson, NCBI-NIH, Bethesda, USA Martin Bishop, Medical Research Council, HGMP, Cambridge, UK Miklos Cserzo, Institute of Enzymology, Budapest, Hungary Reinhard Doelz, Biozentrum, Basel, Switzerland David Judge, University of Cambridge, Cambridge, UK Jack Leunissen, University of Nijmegen, The Netherlands Peter Rice, EMBL, Heidelberg, Germany Cecilia Saccone, University of Bari, Bari, Italy Gyorgy Simon, ICGEB Trieste, Italy Topics: Introduction to Computer Operating Systems Computer Communications, Networking, File Transfer, Electronic Mail, Bulletin Boards Molecular Biology Databases Sequence Homology Searches, Alignments Multiple Alignment, PCR Primer Design Sequence Patterns, Distant Protein Homologies Molecular Evolution: Quantitative and Qualitative Aspects Genome Projects Registration is limited to 30 participants. Prerequisites: Participants must have a basic knowledge of biochemistry and molecular biology, a basic familiarity with computer uses and a need for DNA or protein sequence analysis for their ongoing research. In order to apply, submit the below participation form via e-mail, FAX or normal mail to Ms. Diana Viti, ICGEB, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757333, Fax: +39-40-226555, Telex: 460396 ICGEBT I, Email: viti@icgeb.trieste.it Closing date for applications 31 May 1993. ICGEB will provide accommodation and local hospitality to participants from ICGEB Member Countries. Travel to and from Trieste will normally be borne by the participants. There is no registration fee. ICGEB MEMBER COUNTRIES: Afghanistan, Algeria, Argentina, Bhutan, Bolivia, Brazil, Bulgaria, Chile, China, Colombia, Congo, Costa Rica, Croatia, Cuba, Ecuador, Egypt, Greece, Hungary, India, Indonesia, Iran, Iraq, Italy, Kuwait, Mauritania, Mauritius, Mexico, Morocco, Nigeria, Pakistan, Panama, Peru, Poland, Russia, Senegal, Sri Lanka, Sudan, Syria, Thailand, Trinidad & Tobago, Tunisia, Turkey, Venezuela, Viet Nam, Yugoslavia, Zaire --- Cut here --- ___________________________________________________________________________ INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY MEETINGS * COURSES * WORKSHOPS PARTICIPATION FORM (viti@icgeb.trieste.it) ___________________________________________________________________________ MEETING/COURSE/WORKSHOP.TITLE COMPUTER METHODS IN MOLECULAR BIOLOGY, 14-23 JULY, 1993 ___________________________________________________________________________ DATES............| LOCATION.........| ___________________________________________________________________________ SURNAME..........| FIRSTNAME........| SEX..............| DATE.OF.BIRTH....| AGE..............| COUNTRY.OF.BIRTH.| NATIONALITY......| ___________________________________________________________________________ FULL.BUSINESS.ADDRESS ___________________________________________________________________________ TELEPHONE.NUMBER.| FAX.NUMBER.......| TELEX.NUMBER.....| E-MAIL.ADDRESS...| ___________________________________________________________________________ HOW.WILL.YOUR.RESEARCH.BENEFIT.BY.YOUR.PARTICIPATION.IN.THE.MEETING/COURSE/ WORKSHOP.(NO.MORE.THAN.5.LINES.OF.TEXT) ___________________________________________________________________________ RESEARCH.AREA.OF.INTEREST ___________________________________________________________________________ PRESENT.POSITION ___________________________________________________________________________ ACADEMIC.QUALIFICATIONS.(DEGREE/YEAR/INSTITUTE) ___________________________________________________________________________ INSTITUTES.OF.WORK.SINCE.FORMAL.EDUCATION ___________________________________________________________________________ FELLOWSHIPS.HELD ___________________________________________________________________________ PREVIOUSLY.ATTENDED.ICGEB.MEETINGS/COURSES/WORKSHOPS ___________________________________________________________________________ SHORT.LIST.OF.RELEVANT.PUBLICATIONS ___________________________________________________________________________ From owner-embldatabank@net.bio.net Thu Apr 22 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!howland.reston.ans.net!darwin.sura.net!fconvx.ncifcrf.gov!mayhew From: mayhew@ncifcrf.gov (George Mayhew) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Wanted: SEC2 sequence Message-ID: Date: 23 Apr 93 00:13:12 GMT Organization: Frederick Cancer Research and Development Center Lines: 12 Xref: biosci bionet.molbio.genbank:1271 bionet.molbio.embldatabank:172 Fellow Netters, I have been searching in vain for the gene/protein sequence of Staphylococcal Enterotoxin C2. GenBank and EMBL have the sequences for C1 and C3 databased, but not C2. Neither have I found any literature where someone has cloned or sequenced the C2. As far as I know, neither has anyone sequenced the peptide. I was wondering if someone out there has and has not published the data, or if its been done, and I can't find it. If you have this sequence, would you consider sending it to me. Thanks, George mayhew@ncifcrf.gov From owner-embldatabank@net.bio.net Sun Apr 25 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!mcsun!uknet!comlab.ox.ac.uk!oxuniv!oxpath!rpgrant From: rpgrant@molbiol.ox.ac.uk Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Re: Wanted: SEC2 sequence Message-ID: <1993Apr23.124946.1@molbiol.ox.ac.uk> Date: 23 Apr 93 11:49:46 GMT References: Organization: Oxford University Molecular Biology Data Centre Lines: 31 Xref: biosci bionet.molbio.genbank:1276 bionet.molbio.embldatabank:173 Nntp-Posting-Host: kasia Nntp-Posting-User: rpgrant NCBI Entrez gave the following refs Hovde et al. (1990) Mol Gen Genet 220:329-33 Bohach and Schlievert (1989) Infect Immun 57:2249-52 The latter gives the C2 precursor in the PIR database, accession A60114. The first paper compares the sequence with C1 and C3. I will send you the C2 sequence file. Richard In article , mayhew@ncifcrf.gov (George Mayhew) writes: > Fellow Netters, > I have been searching in vain for the gene/protein sequence of > Staphylococcal Enterotoxin C2. GenBank and EMBL have the sequences for C1 > and C3 databased, but not C2. Neither have I found any literature where > someone has cloned or sequenced the C2. As far as I know, neither has anyone > sequenced the peptide. I was wondering if someone out there has and has > not published the data, or if its been done, and I can't find it. If you have > this sequence, would you consider sending it to me. > > Thanks, > George > mayhew@ncifcrf.gov > -- R. P. Grant <>< rpgrant@molbiol.ox.ac.uk Sir William Dunn School of Pathology Fax. +44 865 275556 University of Oxford, UK. Tel. +44 865 275565 "It's easy when you know how" From owner-embldatabank@net.bio.net Wed Apr 28 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!gatekeeper.us.oracle.com!decwrl!wupost!bcm!usenet From: steffen@mbcr.bcm.tmc.edu (David Steffen) Newsgroups: bionet.molbio.genbank,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.gdb,bionet.molbio.genome-program Subject: Can Genbank and PIR accession numbers ever be the same? Message-ID: <1rmtql$pjg@gazette.bcm.tmc.edu> Date: 28 Apr 93 21:43:49 GMT Organization: Baylor College of Medicine, Houston, Tx Lines: 27 Xref: biosci bionet.molbio.genbank:1279 bionet.molbio.bio-matrix:399 bionet.molbio.embldatabank:174 bionet.molbio.gdb:60 bionet.molbio.genome-program:459 NNTP-Posting-Host: mbcr.bcm.tmc.edu I am working on an oncogene database which includes, among other things, a list of Genbank and PIR sequences of each gene. I am assuming, based on what I have read on this list that Genbank, EMBL, and DDBJ all use the same accession number for the same sequence so that the list of Genbank accession numbers gives access to all three databases. My question is, will a Genbank sequence and a PIR sequence ever have the same accession number - that is, do I need to use both the accession number and the database to insure a unique key? I would be glad to hear from anyone, but mostly am looking for a definitive answer from someone in authority. P.S. I have just put a preliminary version of my database up under gopher. This gopher is not yet linked to gopherspace (via the main Baylor gopher) but should be "Real Soon Now". In the mean time, y'all can gopher on over to mbcr.bcm.tmc.edu and check it out. THANKS! -- David Steffen Department of Cell Biology, Baylor College of Medicine, Houston TX 77030 Telephone = (713) 798-6655, FAX = (713) 790-0545 Internet = steffen@bcm.tmc.edu From owner-embldatabank@net.bio.net Wed Apr 28 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!uunet!utcsri!newsflash.concordia.ca!sifon!monod!francis From: francis@monod.Biol.McGill.CA (Francis Ouellette) Newsgroups: bionet.molbio.genbank,bionet.molbio.bio-matrix,bionet.molbio.embldatabank,bionet.molbio.gdb,bionet.molbio.genome-program Subject: Re: Can Genbank and PIR accession numbers ever be the same? Message-ID: Date: 29 Apr 93 03:23:09 GMT References: <1rmtql$pjg@gazette.bcm.tmc.edu> Sender: news@sifon.cc.mcgill.ca Organization: McGill University Lines: 23 Xref: biosci bionet.molbio.genbank:1280 bionet.molbio.bio-matrix:400 bionet.molbio.embldatabank:175 bionet.molbio.gdb:61 bionet.molbio.genome-program:461 (I am not sure about all this cross-posting, but here it goes anyway!) steffen@mbcr.bcm.tmc.edu (David Steffen) writes: >My question is, will a Genbank sequence and a PIR sequence ever have >the same accession number - that is, do I need to use both the >accession number and the database to insure a unique key? not that I am really in authority, but I think I can quickly see that there are many Genbank/EMBL entries which have many Swiss-Prot/PIR entries assciated with them ... CHIII of yeast comes to mind, but many many others do to. A DNA sequence entry is not just one Open Reading Frame, but a protein sequence entry usualy is. regards, francis -- | B.F. Francis Ouellette * francis@monod.biol.mcgill.ca * | | "Je cherche a` comprendre" Jacques Monod