From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!PRESTO.IG.COM!consult From: consult@PRESTO.IG.COM (Technical Consultant) Newsgroups: bionet.molbio.embldatabank Subject: test Message-ID: Date: 8 Mar 90 17:33:16 GMT Sender: daemon@genbank.BIO.NET Lines: 1 test From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!EMBL-HEIDELBERG.DE!David.Hazledine From: David.Hazledine@EMBL-HEIDELBERG.DE (David Hazledine) Newsgroups: bionet.molbio.embldatabank Subject: Re: Can AUTHORIN be used to submit sequences to EMBL? Message-ID: <24430466E0A00307@EMBL-Heidelberg.DE> Date: 13 Jan 92 10:32:00 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 21 Brian Fristensky writes: > Having used AUTHORIN to submit sequences to GenBank, I am disappointed that > no similar program is available for EMBL. The convenience of data entry, > as well as the consistency of data presentation make this a very useful > tool. > > Recognizing that EMBL can't make direct use of AUTHORIN's transaction-format > files, it seems to me that submission of AUTHORIN-generated EMBL entries should > still be preferable to having to fill out the electronic data submission > form, which is more prone to errors than use of AUTHORIN. I don't know where you got your information from, Brian, but EMBL *can* make use of the output files generated by Authorin, and we welcome Authorin submissions. There is absolutely no problem. Authorin was developed by GenBank with the full support of EMBL and DDBJ, for exactly the reasons you state above, and we are delighted that the software has proven to be as popular as it has. David Hazledine Database Administrator EMBL Data Library. From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!wupost!uunet!bonnie.concordia.ca!ccu.umanitoba.ca!frist From: frist@ccu.umanitoba.ca Newsgroups: bionet.molbio.embldatabank Subject: Can AUTHORIN be used to submit sequences to EMBL? Message-ID: <1992Jan10.211726.8194@ccu.umanitoba.ca> Date: 10 Jan 92 21:17:26 GMT Sender: news@ccu.umanitoba.ca Organization: University of Manitoba, Winnipeg, Manitoba, Canada Lines: 22 Originator: frist@niven.cc.umanitoba.ca Nntp-Posting-Host: niven.cc.umanitoba.ca Having used AUTHORIN to submit sequences to GenBank, I am disappointed that no similar program is available for EMBL. The convenience of data entry, as well as the consistency of data presentation make this a very useful tool. Recognizing that EMBL can't make direct use of AUTHORIN's transaction-format files, it seems to me that submission of AUTHORIN-generated EMBL entries should still be preferable to having to fill out the electronic data submission form, which is more prone to errors than use of AUTHORIN. Would anyone from EMBL care to make a policy statement regarding submission of AUTHORIN-generated EMBL entries? =============================================================================== Brian Fristensky | I'm carrying the weight of all the useless Department of Plant Science | junk a modern man accumulates University of Manitoba | Winnipeg, MB R3T 2N2 CANADA | I'm a statistic in a system frist@ccu.umanitoba.ca | that a civil servant dominates Office phone: 204-474-6085 | FAX: 204-275-5128 | Billy Joel - Running on Ice =============================================================================== From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!CSHL.ORG!theiss From: theiss@CSHL.ORG (Bobbie Theiss in Grace) Newsgroups: bionet.molbio.embldatabank Subject: Thanks for the info Message-ID: <9104172042.AA22557@cshl.org> Date: 17 Apr 91 20:42:00 GMT Sender: daemon@genbank.bio.net Lines: 25 Thank you to everyone that sent me info about how to find the EMBL sequence. I had already tried search@genbank.bio.net, but since I was under the impression that it was recently published I wanted to search the EMBL databanks directly. I received several responses that said to use netserv@embl.bitnet and netserv@embl-heidelberg.de. Both of these worked from my internet address. It winds up that it was not recently published, it was submitted to EMBL "last summer" by someone's "old supervisor". The person who originally asked me how to find it is now in contact with the people at nethelp@embl.bitnet. It could very well be that it they have the wrong accession #. Thanks again, it's amazing how fast the netserver at EMBL & search at GenBank can be. (It's also amazing how many journals are in NEWCITATION.NDX) Bobbie Theiss User Liaison v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v Cold Spring Harbor Laboratory Voice: (516) 367-8390 Box 100 Fax: (516) 367-9576 1 Bungtown Road Internet: Cold Spring Harbor, NY 11724-2213, USA ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!PUCC.PRINCETON.EDU!CBRAUN%HAMPVMS From: CBRAUN%HAMPVMS@PUCC.PRINCETON.EDU Newsgroups: bionet.molbio.embldatabank Subject: Engrailed Homeobox Gene Evolution Message-ID: <9104102218.AA21497@genbank.bio.net> Date: 10 Apr 91 19:35:00 GMT Sender: daemon@genbank.bio.net Lines: 6 Hello, I am attempting to reconstruct the phylogeny of Engrailed like homeobox genes, using distribution data and published sequence information. I have been unable to locate sequences for some taxa, which I believe have been sequenced. These include the second engrailed gene in Zebrafish, ChickEn, Human, and honeybee sequences. I would be extremely grateful for any information on these sequences (accession numbers, etc.) Thank You From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!PUCC.PRINCETON.EDU!MARY007%ARIZRVAX From: MARY007%ARIZRVAX@PUCC.PRINCETON.EDU Newsgroups: bionet.molbio.embldatabank Subject: Information request Message-ID: <9104102123.AA18067@genbank.bio.net> Date: 10 Apr 91 21:19:00 GMT Sender: daemon@genbank.bio.net Lines: 6 Dear Sir: We need information concerning the DNA sequence for the EcoR1-I fragment of EBV B95-8. Could you please send us information via our bitnet address concerning how we could utilize your service to obtain this information? Thank you for your time and consideration - Adrian Winters and Rich Seftor From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!EMBL-HEIDELBERG.DE!NETHELP From: NETHELP@EMBL-HEIDELBERG.DE Newsgroups: bionet.molbio.embldatabank Subject: EMBL File Server News, No. 5, June 26th 1991 Message-ID: <549842A6C49F4002E7@EMBL-Heidelberg.DE> Date: 26 Jun 91 16:57:00 GMT Sender: cook@genbank.bio.net Distribution: bionet Lines: 209 ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 5, June 26th 1991 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 6900 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Updates to data collections <3> Updates to software collection <4> Other updates <5> Summary of contents of file server <6> Getting started ? <1> Introduction ------------- The EMBL File Server Newsletter summarises changes to the EMBL File Server. This newsletter and older issues are available from the server (eg. GET DOC:EMBL_Server_News.2). <2> Updates to Data Collections ------------------------------------ tRNA - We have added a compilation of tRNA sequences from Mathias Sprinzl at the University of Bayreuth, Germany. The database files are located in the file server directory TRNA. Sprinzl M., Dank N., Nock S., Schon A. (1991) Nucl. Acids Res. 19, Supplement, 2127-. PROTEINDATA - A database of homology-derived protein secondary structures (HSSP) has been added, supplied by Chris Sander and Reinhard Schneider (Protein Design Group, EMBL). The database is a merger of 3-D structure information from the Protein Data Bank (PDB) and sequence information from SwissProt (see Proteins 9, 56-68 (1991)). There is one file for each PDB protein containing all protein sequences deemed homologous to this protein, in the form of multiple sequence alignments. Example: get PROTEINDATA:1PPT.HSSP (for pancreatic polypeptide ) The DSSP database of secondary structures has been extended by extracting secondary structure assignments for 28 proteins for which only C(alpha) coordinates have been deposited. This was done with the aid of a model building proc edure that adds backbone coordinates to a C(alpha) trace (L.Holm and C.Sander, J.Mol.Biol. 218, 183-194 (1991)). Example: get PROTEINDATA:3p21.dssp_ca (for p21 ras) Use DIR PROTEINDATA command to get for more information about PDB, DSSP and HSSP-related data files and programs. Just about every existing collection has been updated since the last newsletter so we will not detail them here. The current versions of all collections are detailed below. <3> Updates to Software Collection ------------------------------ Here is a list of new (N) molecular biological programs or updates (U): DOS: ---- PROGRAPH.UAA (N) Protein sequence analysis package (K. Hoffmann) CUTCOST.UAA (U) Program to determine the cheapest source for restriction enzymes v2.31 (C.G. Meinhof) Mac: ---- Plota protein sequence analysis package (A. Luttke, P. Markiewicz) (N) PLOTA_AADATA.HQX Sequence editor PLOTA_DOT.HQX Dot matrix comparison PLOTA_GGR.HQX Secondary structure prediction PLOTA_GOR.HQX Secondary structure prediction PLOTA_HEL.HQX Helical wheel PLOTA_HYD.HQX Hydropathy analysis PLOTA_HYD5.HQX Hydropathy analysis (averaging) PLOTA_KAS.HQX Chain flexibility and antigenicity PLOTA_KKD.HQX Prediction of membrane spanning regions PLOTA_POW.HQX Power spectrum plot PLOTA_SIG.HQX Signal peptide prediction PLOTA_SIM.HQX Dissimilarity plot PLOTA_TMH.HQX Hydrophobic moment analysis DBCONV.HQX (N) Tool for reformatting "line-type" databases to tab-delimited format (J.R. Valverde) EMBL-SEARCH.HQX (N) Simple database retrieval program demonstrating the use of the EMBL CD-ROM indices (R. Fuchs) SEQSPEAK.HQX (N) Sequence data entry with acoustic feedback (K. Conover) TRNA-SEARCH.HQX (N) Identification of tRNA genes and plotting of RNA structure (R.D. Shortridge) DNATRANSLATOR.HQX (U) Version 0.99.1 of the phylogenetic analysis HyperCard stack (D.J. Eernisse) MACMOLECULE.HQX (U) 3D models of biomolecules v1.5 (E. Myers et al.) MACPATTERN.HQX (U) Protein pattern searching with Prosite, v1.2.5 (R. Fuchs) MACTARGSEARCH.HQX (U) Program to search DNA sequences with sequence profiles v2.0 (J.A. Goodrich, W.R. McClure, M.L. Schwartz) UNIX: ----- HOMOCHART.UUE (N) Nice plotting of multiple alignments (R. Smith) OVERSEER.UUE (N) Nucleic acid sequence database analysis package (P. Sibbald) VAX: ---- BOXSHADE.UUE (N) Nice plotting of multiple aligments (K. Hoffmann) DBCONV.HQX (N) Tool for reformatting "line-type" databases to tab-delimited format (J.R. Valverde) OVERSEER.UUE (N) Nucleic acid sequence database analysis package (P. Sibbald) SCRUTINE.UAA (U) Scrutineer protein sequence database analysis package, version May 1991 (P. Sibbald) <4> Other updates ------------- DOC - BIOSCI.DOC April 1991 version of the BIOSCI bulletin-board description. - ORDERFORM.TXT EMBL Data Library subscription form 1991/2 - ORDERINFO.TXT EMBL Data Library subscription information for 1991/2 - CDROM_INDEX.HQX Description of binary indices provided on current EMBL CD-ROMs for access to sequence database files. This is a Macintosh MS Word 4.0 document compressed and converted to ascii by Stuffit. ALIGN - DS6900.UUE Alignment of pseudoeta-globin genes and surrounding sequences from primates and goat. by W. Bailey, Wayne State Univ, Detroit. <5> Summary of Directories of the EMBL File Server ------------------------------------------- Databases (* = new or updated): * EMBL Nucleotide Sequence Database NUC (Rel. 27, May 91 + new data from EMBL/GenBank/DDBJ) * Eukaryotic Promotor Database (Rel. 27, May 91) EPD * SwissProt Protein Database (Rel. 18, May 91) PROT * Prosite pattern database (Rel. 7.00, May 91) PROSITE * ENZYME database (Rel. 5, May 91) ENZYME Brookhaven Protein Structure Database (Rel. 54, Nov 90) PROTEINDATA * REBASE, Restriction Enzyme Database (Rel. 9106, Jun 91) REBASE * tRNA sequence and gene sequence database (1991) TRNA * TFD, Transcription Factor Database (Ver 3.0, Jun 91) TFD * The E.coli Database (Rel. 7, May 91) ECD Drosophila Genetic Map Database (Rel. 9012, Dec 90) DROSOPHILA Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB * Sequence analysis bibliography (SEQANALREF Rel. 17, Jun 91) REFLIST * Functional Analysis of Nucleotide Sequences bibliography REFLIST (FANS_REF Rel. 3.4, Apr 91) Alu sequence database and alignment ALU Software: Software for MS-DOS computers DOS_SOFTWARE Software for Apple Macintosh MAC_SOFTWARE Software for UNIX UNIX_SOFTWARE Software for VAX/VMS VAX_SOFTWARE Other software, GenBank Clearinghouse, etc. MISC_SOFTWARE Miscellaneous: Technical documents, submission and order forms, etc. DOC Multiple DNA sequence alignments and consensus sequences ALIGN Codon Usage tables CODONUSAGE <6> Getting Started ? ----------------- The EMBL File Server is a facility available on the EMBL computing system for external users to request files by electronic mail. The service is free. For initial information, send standard electronic mail to the address: NetServ@EMBL-Heidelberg.DE containing just the word HELP on a line by itself. No essays please. For human contact, send electronic mail to NetHelp at the address(es) given above. From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!CSHL.ORG!theiss From: theiss@CSHL.ORG (Bobbie Theiss in Grace) Newsgroups: bionet.molbio.embldatabank Subject: looking for a sequence Message-ID: <9104122159.AA24264@cshl.org> Date: 12 Apr 91 21:59:05 GMT Sender: daemon@genbank.bio.net Lines: 17 where can I retrieve an EMBL sequence that was just recently published? (2 weeks ago) I've looked thru Archie for 'embl' but only found an FTP site in Europe to download sections of the EMBL databank. I have an accession #. Thanks Bobbie Theiss User Liaison v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v v Cold Spring Harbor Laboratory Voice: (516) 367-8390 Box 100 Fax: (516) 367-9576 1 Bungtown Road Internet: Cold Spring Harbor, NY 11724-2213, USA ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!rutgers!phri!cmcl2!mcclb0.med.nyu.edu!hill From: hill@mcclb0.med.nyu.edu Newsgroups: bionet.molbio.embldatabank Subject: Help finding a sequence Message-ID: <1991Oct11.081027.7034@mcclb0.med.nyu.edu> Date: 11 Oct 91 12:10:27 GMT Organization: NYU Medical Center, New York, NY, USA Lines: 22 We are looking for a sequence published in FEBS Letters (1991) 278(2):211-216. The title of the article is "Cloning and functional expression of a TEA-sensitive A-type potassium channel from rat brain." The authors are: Klaus-Hasso Schroeter, Johann Peter Ruppersberg, Frank Wunder, Jens Rettig, Martin Stocker, and Olaf Pongs. No accession number was given, but according to the Fig. 1 on page 212, the "composite Raw3 sequence was submitted to EMBL." Checking our local database, which is updated nightly from the sequences on Usenet, and the EMBL & EMBL New Data sections of the GenBank Online Service no such sequence is among the released sequences (as of 11-OCT-1991 08:00 EDT). Could you please check to see if the sequence is being held until publication or otherwise waiting for release? Only the protein sequence was published, so until it is released by EMBL, the DNA sequence is unavailable to the scientific community. Danke schoen! John Edward Hill, Ph.D. | Department of Cell Biology Internet: HILL@MCCLB0.MED.NYU.EDU | New York University Medical Center EARN/Bitnet: HILL@NYUMED.BITNET | 550 Fifth Avenue 212-263-7135 FAX: 212-263-8139 | New York, New York 10016-6402 From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!lhc!nih-csl!helix.nih.gov!donnel From: donnel@helix.nih.gov (Donald A. Lehn) Newsgroups: bionet.molbio.embldatabank Subject: NIH Database Message-ID: <1173@nih-csl.nih.gov> Date: 3 Apr 91 20:36:06 GMT Sender: news@nih-csl.nih.gov Distribution: bionet.molbio.embldatabank Organization: National Institutes of Health, Bethesda Lines: 37 To all networked researchers: I am in the process of putting together an NIH research proposal for a grant to establish a national net accessible NIH database. This database would be accessible by anonymous FTP by anyone on this network. The data base would contain amung other things: 1. Detailed experimental protocols. 2. Listings of sources of reagents, vectors, and any other materials, both commercial and from individuals, that may be needed by NIH researchers. 3. Information on grants. What grants are avaliable. Help files. And a listing of the current grants and contracts. 4. A job bank. 5. Software developed by NIH researchers who wish to have others share in it use. If you are interested in seeing such a database established please send me an E-mail message indicating such. Also please state what other types of data you would like to see included in such a database. Since I plan on using these replies in my grant application, please be sure to include your full name, position, affiliation and phone number in your response. Thanking you in advance, Donald A. Lehn National Cancer Institute National Institutes of Health Bethesda, MD 20892 Pnone: (301) 496-2885 FAX: (301) 468-8419 E-mail: donnel@helix.nih.gov From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!arcb.afrc.ac.uk!ODONNELL From: ODONNELL@arcb.afrc.ac.uk (Cary O'Donnell) Newsgroups: bionet.molbio.embldatabank Subject: EMBL dbase reference Message-ID: <9109051515.AA06851@genbank.bio.net> Date: 5 Sep 91 16:07:00 GMT Sender: ryals@genbank.bio.net Distribution: bionet Lines: 17 Is there an 'official' reference to the EMBL nucleotide database and SWISSPROT? If it's in the distribution tapes, as I haven't been able to find it, please point me to the correct file. thanks ***************************************************************************** AFRC Computing Division JANET : AFRC.ARCB::ODONNELL West Common INTERNET: ODONNELL@ARCB.AFRC.AC.UK Harpenden Tel: (+44) 582 762271 ext 229 Herts AL5 2JE Fax: (+44) 582 761710 U.K. (AFRC = Agricultural & Food Research Council) ----------------------------------------------------------------------------- From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!news.cs.indiana.edu!att!pacbell.com!mips!apple!news.bbn.com!bbn.com!news From: news@bbn.com (News system owner ID) Newsgroups: bionet.general,bionet.molbio.embldatabank Subject: New "Kabat Book" now available Message-ID: <67449@bbn.BBN.COM> Date: 19 Nov 91 20:47:44 GMT Reply-To: hperry@BBN.COM () Followup-To: bionet.followup,bionet.molbio.embldatabank Organization: Bolt Beranek and Newman Inc., Cambridge MA Lines: 67 Xref: bionet bionet.general:1787 bionet.molbio.embldatabank:68 New "Kabat Book" now available We are pleased to announce that the 5th edition of "Sequences of Proteins of Immunological Interest" is now available. It is comprised of three volumes that exceed 2500 pages. Contents include over 400 groupings of related amino acid and nucleotide sequences of: - signal sequences of light chains, heavy chains, T-lymphocyte receptors, related proteins - variable region of light chains, heavy chains, T-lymphocyte receptors for antigen - constant region - major histocompatibility antigens Class I - I region gene products Class II - related proteins - D and J minigenes - Pseudogenes In addition to a lengthy introduction, this edition contains new and expanded sections on T-cell receptors, B2-microglobulins, major histocompatibility antigens, complement, thymopoietin, integrins and post-gamma globulin. Also included are summary distribution tables, variability plots, and comprehensive indices for protein names, antibody specificities and references. "Sequences of Proteins of Immunological Interest" (NTIS PB91-192898) is a non-profit book distributed by the National Technical Information Service (NTIS). There is a small charge for this edition to cover the costs of distribution. For domestic delivery, the price is $30. For international delivery, the price is $51 (surface delivery) and $67 (air express). Call the sales desk at 703-487-4650 or fax the appended order form to 703-321-8547. You will be invoiced at the time of delivery. ------------------------------------------------------------------ NTIS Order Form U.S. Department of Commerce National Technical Information Service 5285 Port Royal Road Springfield, VA 22161 Name: Title: Company/Organization: Address: City/State/Zip: Telephone: Please reserve a copy of the 5th edition of "Sequences of Proteins of Immunological Interest" for me. (NTIS PB91-192898) (check only one) U.S. Delivery - $30: International Delivery - surface - $51: International Delivery - air express - $67: You will be invoiced at the time of delivery FAX this form to 703-321-8547 From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!cs.utexas.edu!uunet!mcsun!unido!uni-koeln!news From: KHOFMANN@cipvax.biolan.Uni-Koeln.DE (Kay Hofmann) Newsgroups: bionet.molbio.embldatabank Subject: double submission better than single ones? Message-ID: <1991Aug23.082214.170460@rrz.uni-koeln.de> Date: 23 Aug 91 08:22:14 GMT Sender: news@rrz.uni-koeln.de (Usenet News System) Organization: University of Cologne, FRG (Biolan) Lines: 9 X-News-Reader: VMS NEWS 1.12 A simple (maybe stupid) question: If i submit a new sequence to EMBL, is it desirable to submit the same sequence to genbank also or is it better to let the organisations exchange their data? I think that there are consistent accession numbers for a single sequence in all databases, so if i do a double submission, how do EMBL/genbank take care of consistency of accession numbers? Thank you, Kay Hofmann From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!vax1.computer-centre.birmingham.ac.uk!HUENSD From: HUENSD@vax1.computer-centre.birmingham.ac.uk Newsgroups: bionet.molbio.embldatabank Subject: Macplasmap/Norton Utilities Disk Assistance Incompatibility Message-ID: <9106211650.AA19645@genbank.bio.net> Date: 21 Jun 91 21:08:00 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 18 I have encountered problems when attempting to use the MacPlasmap program version 1.82 (downloaded from EMBL server) when the Norton Utilities for the Macintosh-Disk Assistance is also installed in the same machine. The problem shows up as an inability to save any files created. Further attempts may crash the system altogether. The problem can be avoided by removing the Directory Assistance (not Disk Assistance as shown above - typo error) application from the system file. I don't know why it happens and I'm not going to find out but this workaround will at least allow the use of MacPlasmap! Has anyone else encountered it? David Huen e-mail: JANET: huensd%uk.ac.bham.vax1 snail: Dept. of Cancer Studies, Univ. of Birmingham, B15 2TJ, U.K. From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!apple!mips!spool.mu.edu!munnari.oz.au!ariel!ucsvc.ucs.unimelb.edu.au!wehi.dn.mu.oz!tony From: tony@wehi.dn.mu.oz Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Has anyone got the PYAC4 vector sequence? Message-ID: <1991Jul8.122232.24651@wehi.dn.mu.oz> Date: 8 Jul 91 12:22:32 GMT Organization: Walter & Eliza Hall Institute Lines: 19 Xref: bionet bionet.molbio.genbank:455 bionet.molbio.embldatabank:54 Posted: Mon Jul 8 07:22:32 1991 We have a user who is looking for the complete PYAC4 vector sequence. We cannot find it in any of the databases. We have a less than perfect quality FAX with the 11171 bases but would rather not have to type up such a sequence given the degree of uncertainty in some sections of the FAX. Has anyone got it on file, and could mail it to us please? Should artificial sequences such as these make it to the databases? The sequence has been around for a while. ================================================================================ Dr. Tony Kyne, Head, Computer Sciences Unit, The Walter and Eliza Hall Institute of Medical Research, P.O. Royal Melbourne Hospital, Victoria, 3050, Australia. Phone: International +61-3-345-2586 FAX: International +61-3-347-0852 National 03-345-2586 National 03-347-0852 Email: Internet: tony@wehi.edu.au OR tony@wehi.dn.mu.oz.au PSIMAIL: PSI%0505233430002::tony =============================================================================== From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!apple!mips!zaphod.mps.ohio-state.edu!wupost!uunet!bonnie.concordia.ca!ccu.umanitoba.ca!frist From: frist@ccu.umanitoba.ca Newsgroups: bionet.molbio.embldatabank Subject: Keeping GenBank/EMBL/DDBJ Software-Parseable Message-ID: <1991Sep15.212007.16479@ccu.umanitoba.ca> Date: 15 Sep 91 21:20:07 GMT Organization: University of Manitoba, Winnipeg, Canada Lines: 129 I am not one to complain, as those familiar with my postings will attest, and I am particularly hesitant to criticize those who oversee the major databases GenBank, which, in my opinion, have made great progress in recent years with the introduction of the DDBJ/EMBL/GenBank Feature Table format. However, I percieve a philosophical shift which to me undermines much of that progress. BACKGROUND, FOR THOSE NOT FAMILIAR WITH THE FEATURES TABLE FORMAT ------------------------------------------------------------------ When the databases were first released using the new Features format, this was perhaps the most significant step ever towards making the data machine-accessible. In place of the old, difficult-to-parse Features table was, in effect, a fairly rigorously-defined programming language. For example an mRNA comprised of three exons could be constructed by evaluating a very simple expression: join(78..348,372..495,530..712) The power of this language is that a single parsing algorithm can create ANY feature! Each expression evaluates to a sequence. I'll repeat that because it is the crux of the matter: "EACH EXPRESSION EVALUATES TO A SEQUENCE" Thus, the more features that are formulated as expressions, the more features that can be retrieved by software. In other words, the utility of the database is increased as more features are encoded into the language. RECENT CHANGES IN THE ENCODING OF FEATURES ------------------------------------------ The GenBank entry BRLTRPLE (M17892) illustrates the way in which the utility of the database can be decreased by how annotation is implemented. When the new Features format was first implemented, a mutant containing two point mutations was defined in the expression variation group(r1,r2) /label=mutant_1041 where r1 and r2 referred to two features, identified by the unique labels r1 and r2, which contained the expressions replace(207,"a") and replace(443,"c") The utility of constructs like this has been realized in my program GETOB, which is able to evaluate virtually any Feature expression and return the resultant feature. For example, an expression such as M17892:group(1..934,mutant_1041) would retrieve the entire 934bp sequence, modified according to the labeled expression. Contrast the old construct with the way it is currently implemented: variation 207..207 /note="g in AJ23036; a in mutant 1041" variation 443..443 /note="a in AJ23036; c in mutant 1041" I have several problems with this. First, the expression given doesn't evaluate to anything new. 207..207 returns the WILD TYPE allele at that position. Secondly, the mutant sequences have been split up into two separate features. This is a step backwards from the original Features philosophy, which sought to put together previously disconnected things into single coherent features. Additionally, the previous version made the feature accessible through a /label= qualifier. /label has a specific meaning: it is a tag within an entry that serves as a unique handle on that feature. In contrast, /note= is almost meaningless. This qualifier is for anything whose sole purpose is as a note to the human reader. Most importantly, the relegation of the actual data describing the mutation to a /note means that THAT DATA IS NO LONGER MACHINE READABLE, because, in contrast to the rigorously- defined Features expression, the note has no strict definition. Consequently, you can't write software to access it. IMPLICATIONS ------------ How much data has been effectively lost from software-accessibility because of re-structuring of entries in this fashion? I only discovered this particular change while testing GETOB, in preparation for publication of an article describing XYLEM. In effect, such changes in database presentation, while still consistent with the Features Definition, amount to fundamental changes in the database. How can software developers write software with major upheavals such as these occurring with no prior announcement? (It occurs to me that I was supposed to be on a developer's mailing list. Do the databases ever consult with developers? Many of us spend an awful lot of time thinking about the database, and might have some useful input). CONCLUSION ---------- Many people have little appreciation for what an immensely useful thing the Features language can be, partly because very little software is yet available for utilizing this language. Over the last few years, my XYLEM package has tackled exactly that, starting with the old Features format, and evolving as the new Features format matured. This evolutionary process, in fact, has been the main reason that the publication of my paper on XYLEM has been delayed. The recent additions to the Definition have been very easy to implement, being logical extensions of the already-existing Definition. For example, it took only a few hours to add the /codon_start qualifier to GETOB. In contrast, writeing a routine to dissect information from a /note is a horrendous task at best, and likely to produce an unreliable result. I implore the database directors to keep moving in the direction of getting as much of the data into a software-parsable form. The databases can only reach their true potential when we can minimize the need for human intervention in manipulating pieces of data. Finally, don't develop these things in a vacume. Ask the software developers, and perhaps even the user community in general, what they would like the database to be. The bulletin boards provide a vary simple mechanism for sounding out ideas and getting input from a large number of minds. =============================================================================== Brian Fristensky | Conservation is getting nowhere because it is Department of Plant Science | incompatible with our Abrahamic concept of University of Manitoba | land. We abuse land because we regard it as a Winnipeg, MB R3T 2N2 CANADA | commodity belonging to us. When we see land frist@ccu.umanitoba.ca | as a community to which we belong, we may Office phone: 204-474-6085 | begin to use it with love and respect. FAX: 204-275-5128 | Aldo Leopold, 1948 A SAND COUNTY ALMANAC =============================================================================== From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!VTVM2.CC.VT.EDU!mvoice%uk.ac.crc From: mvoice%uk.ac.crc@VTVM2.CC.VT.EDU (Mr. M.W. Voice) Newsgroups: bionet.molbio.embldatabank Subject: concensus repeat sequences Message-ID: <25857.9110141515@crc.ac.uk> Date: 14 Oct 91 15:15:37 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 10 Does anyone know of a list of concensus sequences I appear to have picked up a CACA repeat which from a search of the EMBL database seems to be a concensus sequence. Any information on this would be greatly appreciated. M.Voice Dept Obs & Gynae Ninewells Hospital & Medical School Dundee DD1 9SY. From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GENBANK.BIO.NET!kristoff From: kristoff@GENBANK.BIO.NET (Dave Kristofferson) Newsgroups: bionet.molbio.embldatabank Subject: Changes coming to BIOSCI Message-ID: Date: 7 May 91 22:51:45 GMT Sender: kristoff@genbank.bio.net Lines: 36 Dear BIOSCI users, I apologize for sending a copy of this to each of the newsgroups, but I need to make sure that all of our e-mail subscribers are notified of an impending reorganization of BIOSCI. It appears that we will be doing some substantive reconfiguration work on BIOSCI in the very near future. I will provide details soon on the BIONEWS/bionet.general newsgroup (where this has previously been discussed), but I am sending this message out now as an alert for the following reasons: 1) if anyone finds that their BIOSCI subscriptions cease, please send a message to me at biosci@genbank.bio.net. It is possible that some addresses may cause problems and may have to be withheld from mailings until clarification is received. You can help us if you notice that you no longer are receiving postings by sending me mail from the address at which you wish to receive bulletins. In the event that you subscribe only to the less frequently used newsgroups, please let a week go by before you conclude that you have been dropped from the mailing list. 2) There is always the possibility when mailing lists are transferred that some problems with duplicates or lost messages may temporarily arise. I'd appreciate your indulgence during the reorganization. We have made substantial progress in the last few days but some details remain to be worked out. I will make further announcements on BIONEWS as developments warrant. Thanks for your cooperation. Sincerely, Dave Kristofferson GenBank Manager kristoff@genbank.bio.net From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!awiuni11.bitnet!A8101GAW From: A8101GAW@awiuni11.bitnet (Michael Szostak) Newsgroups: bionet.molbio.embldatabank Subject: (none) Message-ID: <9108101828.AA26146@genbank.bio.net> Date: 10 Aug 91 18:58:29 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 12 I am using pBluescript KS (plus) for construction of lacZ fusions. By sequencing I found one of the 3 G+s in the KpnI site is missing (nt 756) but inspite of this frame shift mutation, the ability for alpha complementation and blue/white color selection is unaffected. For practical reasons I need urgently an unmutated pKS (plus) (not pBS or pSK or pBluescript II KS (plus)). Is there anyone in Europe who could provide me with a clean plasmid ? Thanks in advance M. Szostak / Inst. f. Mikrobiol. u. Genetik / Althanstr.14 / A-1090 WIEN Austria From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!caen!sdd.hp.com!spool.mu.edu!uunet!brunix!jmm From: jmm@cs.brown.edu (Jim Meyers) Newsgroups: bionet.molbio.embldatabank Subject: Brookhaven data format Message-ID: <67172@brunix.UUCP> Date: 4 Mar 91 18:52:51 GMT Sender: news@brunix.UUCP Reply-To: jmm@cs.brown.edu (Jim Meyers) Distribution: bionet Organization: Brown University Department of Computer Science Lines: 8 Is anyone familiar with the Brookhaven data format for 3D protein structures? If anyone could supply me with a sample, I would be most grateful. Thanks in advance. ___________________________________________________________________________ Jim Meyers | | Brown University Box 1910 | jmm@cs.brown.edu | Providence, RI 02912 | (401)-863-7682 | From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!EMBL-HEIDELBERG.DE!Rainer.Fuchs From: Rainer.Fuchs@EMBL-HEIDELBERG.DE ("Rainer Fuchs ", EMBL Data Library) Newsgroups: bionet.molbio.embldatabank Subject: NEWENTRIES.NDX Message-ID: <50E6FAE4A19F401E74@EMBL-Heidelberg.DE> Date: 1 Jul 91 09:44:00 GMT Sender: kristoff@genbank.bio.net Distribution: bionet Lines: 9 Since June 16, the weekly list of new and updated nucleotide sequence database entries (NEWENTRIES.NDX) has been unavailable, due to a problem with the batch job that creates this list. That problem should now been solved. Thanks to all collegues who pointed this out to us. Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!lhc!ncifcrf!fcs260c2!toms From: toms@fcs260c2.ncifcrf.gov (Tom Schneider) Newsgroups: bionet.molbio.embldatabank Subject: Re: Keeping GenBank/EMBL/DDBJ Software-Parseable Message-ID: <2374@fcs280s.ncifcrf.gov> Date: 17 Sep 91 02:35:49 GMT References: <1991Sep15.212007.16479@ccu.umanitoba.ca> Sender: news@ncifcrf.gov Organization: NCI Supercomputer Facility, Frederick, MD Lines: 18 In article <1991Sep15.212007.16479@ccu.umanitoba.ca> frist@ccu.umanitoba.ca writes: >Most importantly, the relegation of the actual data >describing the mutation to a /note means that THAT DATA IS NO >LONGER MACHINE READABLE, because, in contrast to the rigorously- >defined Features expression, the note has no strict definition. >Consequently, you can't write software to access it. I completely agree. >Brian Fristensky Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!zaphod.mps.ohio-state.edu!wupost!uunet!mcsun!unido!uni-koeln!news From: KHOFMANN@cipvax.biolan.Uni-Koeln.DE (Kay Hofmann) Newsgroups: bionet.molbio.embldatabank Subject: ADDITON to: remainders of vector sequences in nucleotide databases Message-ID: <1991Oct21.103024.171986@rrz.uni-koeln.de> Date: 21 Oct 91 10:30:24 GMT Sender: news@rrz.uni-koeln.de (Usenet News System) Organization: University of Cologne, FRG (Biolan) Lines: 46 X-News-Reader: VMS NEWS 1.12 Hello, Let me add a few comments on my previous posting about remainders of vector sequence stretches in non-vectorial sequences. I just noticed the flaming discussion about correctness of genbank which seems to be led on bionet.general and am afraid that someone could mistake my posting as part of the witch-hunt on database maintainers. As a matter of fact i LIKE the way GENBANK, EMBL and especially SWISSprot are maintained and annotated, at least if one takes the annotation-time into account. So the reasons for my posting were the following: - point the users of DNA-databases towards the fact that there are at the moment vectorial sequences at unusual positions that maight be mistaken as possible repeat sequences becuase they are not ruled out by the standard ways of discarding known repeats/sequence families in the statistical analysis of repeats - ask the database users if they agree that is is undesirable to have those sequences present. In my personal opinion it is not only desirable to remove the vectorial sequences themselves but also linkers and restriction sites that are not occuring in the sequence as it occurs in nature. Another submission strategy would be submitting clones as they are (including vectors linkers, etc.) but i would prefer for 'normal' (not 'syn') entries doing it the first way. - ask data-submitters if they could avoid submitting vector-containing sequences - ask the database maintainers if it is possible to remove those from existing entries. Of course, the vectorial sequences originate from the submitters and this problem is NOT restricted to EMBL-databases. In my last posting i mentioned only EMBL-entries because this is the database i usually query first. Best regards, Kay Hofmann ------------------------------------------------------------------------ Kay Oliver Hofmann Tel. ++49 201 478 6980 Institut fuer Biochemie (med. Fak.) FAX ++49 201 478 6979 Universitaet Koeln Joseph Stelzmann Str. 52 INTERNET: D-5000 Koeln 41 KHOFMANN@cipvax.biolan.uni-koeln.de ------------------------------------------------------------------------ From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!ASRR.ARSUSDA.GOV!dbolt From: dbolt@ASRR.ARSUSDA.GOV ("DOUGLAS BOLT") Newsgroups: bionet.molbio.embldatabank Subject: (none) Message-ID: <9109270144.AA26642@genbank.bio.net> Date: 27 Sep 91 01:35:00 GMT Sender: news@genbank.bio.net Distribution: bionet Lines: 2 subscribe embl-db douglas bolt From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!EMBL-HEIDELBERG.DE!NETHELP From: NETHELP@EMBL-HEIDELBERG.DE Newsgroups: bionet.molbio.embldatabank Subject: EMBL File Server News No. 4, March 21st 1991 Message-ID: <9DED8BB335DF803266@EMBL-Heidelberg.DE> Date: 25 Mar 91 09:13:00 GMT Sender: daemon@genbank.bio.net Lines: 166 ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 4, March 21st 1991 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 6900 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 or 387306 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Updates to data collections <3> Updates to software collection <4> Other updates <5> Common questions <6> Summary of contents of file server <7> Notice of EMBL's withdrawal from Bitnet <8> Getting started ? <1> Introduction ------------- The EMBL File Server Newsletter summarises changes to the EMBL File Server. This newsletter and older issues are available from the server (eg. GET DOC:EMBL_Server_News.2). <2> Updates to Data Collections ------------------------------------ The following data collections have been updated recently: Nuc - Release 26, February 1991, of the EMBL Nucleotide Sequence Database. Prot - Release 17, February 1991, of the SWISS-PROT Protein Sequence Database. ProteinData - A database of homology-derived protein structures (HSSP) supplied by Chris Sander is now available along with the existing Brookhaven PDB and the DSSP secondary structure digest of the PDB protein files. ProSite - Release 6.1 of Amos Bairoch's pattern database. A version of ProSite suitable for use with Scrutineer is now available. Enzyme - Release 4 of Amos Bairoch's enzyme database. ECD - Release 6 of Manfred Kroeger's E.coli database Reflist - Release 15 of Amos Bairoch's sequence analysis bibliography. ReBase - Release 9103 of Rich Roberts's restriction enzyme database. Alu - Jerzy Jurka's Alu Sequence Database, October 1988 The directory NUC is continually updated with nucleotide sequence data from EMBL/GenBank/DDBJ, and the directory PROT is updated with data from the SWISS-PROT protein sequence database. <3> Updates to Software Collection ------------------------------ Here is a list of new (N) molecular biological programs or updates (U): DOS: ---- EASISTAT.UAA (N) Statistical analysis package (D. Curtis) PEDRAW.UAA (N) Pedigree drawing (D. Curtis) Mac: ---- MATMETH.HQX (U) New version 5.0 of Material & Methods stack J. Brown MACREVIEW.1 (N) Two reviews of Mac software in molecular biology MACREVIEW.2 (P. Markiewicz) UNIX: ----- SEQF.UAA (N) Package for searching genetic sequence libraries (D. Davison and M. Kanehisa) VAX: ---- SCRUTINE.UAA (U) New version of SCRUTINEER protein database analysis package (P. Sibbald) CDACCESS.UAA (U) Update (v2.06) of CD-ROM access software (P. Stockwell) <4> Other updates ------------- DOC - BIOSCI.DOC March 1991 version of the BIOSCI bulletin-board description. - SERVER.TXT Michael Gribskov's Molecular Biology FTP and Server List, March 7th 1991. - BIOBIT.19 Rob Harper's newletter, BioBit No. 19: "Archie" ALIGN - DS6748.UUE Alignment of germline VH gene sequences, submitted by W. Mueller, 6-Mar-1991. CODONUSAGE - A collection of codon usage tables in GCG format provided by Mike Cherry. <4> Common questions ---------------- Q: Can I access the EMBL File Server via FTP ? A: Not yet. We are on Internet and await an upgrade to our connection before starting an anonymous ftp service. <6> Summary of Directories of the EMBL File Server ------------------------------------------- Databases: EMBL Nucleotide Sequence Database NUC (Rel. 26, Feb 91 + new data from EMBL/GenBank/DDBJ) Eukaryotic Promotor Database (Rel. 26, Feb 91) EPD SwissProt Protein Database (Rel. 17, Feb 91) PROT Prosite pattern database (Rel. 6.1, Feb 91) PROSITE ENZYME database (Rel. 4, Feb 91) ENZYME Brookhaven Protein Structure Database (Rel. 54, Nov 90) PROTEINDATA REBASE, Restriction Enzyme Database (Rel. 9103, Mar 91) REBASE TFD, Transcription Factor Database (Ver 2.1, Feb 91) TFD The E.coli Database (Rel. 6, Feb 91) ECD Drosophila Genetic Map Database (Rel. 9012, Dec 90) DROSOPHILA Listing of Molecular Biology Databases, LiMB (Rel. 2.0) LIMB Sequence analysis bibliography (SEQANALREF Rel. 15, Feb 91) REFLIST Functional Analysis of Nucleotide Sequences bibliography REFLIST (FANS_REF Rel. 1.3, Nov 90) Alu sequence database and alignment ALU Software: Software for MS-DOS computers DOS_SOFTWARE Software for Apple Macintosh MAC_SOFTWARE Software for UNIX UNIX_SOFTWARE Software for VAX/VMS VAX_SOFTWARE Other software, GenBank Clearinghouse, etc. MISC_SOFTWARE Miscellaneous: Technical documents, submission and order forms, etc. DOC Multiple DNA sequence alignments and consensus sequences ALIGN Codon Usage tables CODONUSAGE <7> Notice of EMBL's withdrawal from Bitnet --------------------------------------- EMBL intends to withdraw from Bitnet as from January 1st 1992. The network address EMBL.Bitnet should function up until that date, but we recommend that users switch to using EMBL-Heidelberg.DE (Internet) from now onwards. <8> Getting Started ? ----------------- The EMBL File Server is a facility available on the EMBL computing system for external users to request files by electronic mail. The service is free. For initial information, send standard electronic mail to the address: NetServ@EMBL-Heidelberg.DE containing just the word HELP on a line by itself. No essays please. For human contact, send electronic mail to NetHelp at the address(es) given above. From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!EMBL-HEIDELBERG.DE!Peter.Stoehr From: Peter.Stoehr@EMBL-HEIDELBERG.DE (Peter Stoehr) Newsgroups: bionet.molbio.embldatabank Subject: EMBL databases - a new subscription year Message-ID: Date: 19 Aug 91 15:39:00 GMT Sender: aley@genbank.bio.net Distribution: bionet Lines: 11 The next release of the EMBL nucleotide database, Release 28, is scheduled for September 1991, and is the first of a new subscription year. We need to receive a new (1991/2) subscription form for orders of this and subsequent releases: we do not carry subscriptions over from one year to the next. This is just a reminder for the many who traditionally forget to send in a new form at this time of year and wait in vain for their new database release. Regards, Peter Stoehr EMBL Data Library From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!GREARN.BITNET!SAVAKIS From: SAVAKIS@GREARN.BITNET (Babis Savakis) Newsgroups: bionet.molbio.embldatabank Subject: (none) Message-ID: <9110150811.AA26647@genbank.bio.net> Date: 15 Oct 91 08:22:56 GMT Sender: news@genbank.bio.net Distribution: bionet Lines: 1 signoff embl-db babis savakis From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!s.u-tokyo!ccut!sun-barr!lll-winken!elroy.jpl.nasa.gov!usc!cs.utexas.edu!news-server.csri.toronto.edu!torsqnt!lsuc!canrem![peter.pawelek@canrem.uucp] From: peter.pawelek@canrem.uucp (peter pawelek) Newsgroups: bionet.molbio.embldatabank Subject: pembl18 Message-ID: <199110.646.24@canrem.uucp> Date: 11 May 91 03:53:13 GMT Reply-To: "peter pawelek" Distribution: bionet Organization: Canada Remote Systems Lines: 7 I am very interested in obtaining a text file of the nucleotide sequence of pEMBL18(or pEMBL8). If anyone out there is in possession of this sequence and is willing to upload it for me, please let me know through this network. Thanx. -- Canada Remote Systems. Toronto, Ontario NorthAmeriNet Host From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!news.cs.indiana.edu!sdd.hp.com!spool.mu.edu!yale.edu!ira.uka.de!chx400!urz.unibas.ch!bioftp.unibas.ch!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.molbio.embldatabank Subject: MacPattern (Was: ftp at ftp.embl-heidelberg.de Message-ID: Date: 28 Sep 92 09:28:02 GMT References: <19pls2INNi56@grasp1.univ-lyon1.fr> <1992Sep24.005109.21258@nmr-z.mgh.harvard.edu> Followup-To: bionet.molbio.embldatabank Organization: EMBL Data Library Lines: 24 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de In article <1992Sep24.005109.21258@nmr-z.mgh.harvard.edu>, cherry@OPAL.MGH.HARVARD.EDU wrote: > The ftp.embl-heidelberg.de ftp site is on a very slow network link to > the outside world. You can retrieve MacPattern from any of the hosts > listed below. This is what archie says is available on macpattern. The list that followed in this message showed one of the weaknesses of Archie: you can't find information about the authorative site for a program. All sites listed had outdated versions, sometimes about 2 years old. I don't want to blame Archie; it can't store more information than is provided. The Internet IAFA working group is currently trying to establish standards for describing ftp archives and their contents which will include "authority" information that could then be picked up by Archie in the future. > The EMBL mail server is still one of the best ways to retrieve files > from Heidelberg. Nothing to add to this. We keep trying to improve our Internet links. Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!news.cs.indiana.edu!sdd.hp.com!spool.mu.edu!yale.edu!ira.uka.de!chx400!urz.unibas.ch!bioftp.unibas.ch!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.molbio.embldatabank,bionet.software Subject: EMBL-Search v2.1 available Message-ID: Date: 28 Sep 92 09:41:35 GMT Organization: EMBL Data Library Lines: 21 Xref: bionet bionet.molbio.embldatabank:111 bionet.software:3340 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de Version 2.1 of EMBL-Search is now available. EMBL-Search is a free database query and retrieval program for the Apple Macintosh for use with the EMBL Sequence Databases CD-ROM. Version 2.1 allows text queries of the PROSITE protein pattern database, in addition to the EMBL nucleotide and SWISS-PROT protein sequence databases. Cross-references between EMBL, SWISS-PROT, PROSITE (data) and PROSITE (doc) can be used to navigate easily between these databases. EMBL-Search requires the December 1991 EMBL CD-ROM or later. For queries of PROSITE, the new September 1992 CD-ROM (Disk 1) is needed. EMBL-Search 2.1 will be provided in binhexed form on the next EMBL CD-ROM. It can also be obtained by electronic mail from NetServ@EMBL-Heidelberg.DE (get mac_software:embl-search.hqx) or by anonymous ftp from ftp.embl-heidelberg.de (/pub/software/mac/embl-search.hqx). The complete source code is available as well (embl-search_src.hqx). Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!rutgers!stanford.edu!hsdndev!nmr-z!OPAL.MGH.HARVARD.EDU!CHERRY From: cherry@OPAL.MGH.HARVARD.EDU Newsgroups: bionet.molbio.embldatabank Subject: Re: ftp at ftp.embl-heidelberg.de Message-ID: <1992Sep24.005109.21258@nmr-z.mgh.harvard.edu> Date: 24 Sep 92 00:51:09 GMT References: <19pls2INNi56@grasp1.univ-lyon1.fr> Sender: usenet@nmr-z.mgh.harvard.edu (User for USENET news postings) Reply-To: cherry@OPAL.MGH.HARVARD.EDU Organization: Molecular Biology - Mass Gen Hospital Lines: 59 Nntp-Posting-Host: opal.mgh.harvard.edu >In article <19pls2INNi56@grasp1.univ-lyon1.fr>, rahbe@jouy.inra.fr (Yvan Rahbe) writes: >>I would like to get MacPattern at the embl ftp site, and I have problem >>in getteing reasonable access time to this server (camparatively to any >>other server). I am using Fetch. Is there a reason for this ? >> >>Thanks >> The ftp.embl-heidelberg.de ftp site is on a very slow network link to the outside world. You can retrieve MacPattern from any of the hosts listed below. This is what archie says is available on macpattern. The EMBL mail server is still one of the best ways to retrieve files from Heidelberg. Mike Cherry cherry@frodo.mgh.harvard.edu Host burgundy.nectar.cs.cmu.edu Location: /readmes/readmes.untared/edu/indiana/bio/fly/molbio/mac FILE -r--r--r-- 1413 Feb 21 02:09 macpattern.readme Host csuvax1.csu.murdoch.edu.au Location: /pub/murphic/mac FILE -rw-r--r-- 971 Jul 6 15:01 macpattern.readme Host evolution.bchs.uh.edu Location: /pub/gene-server/mac FILE -rwxr--r-- 97223 Sep 16 1991 macpattern1.hqx FILE -rwxr--r-- 228430 Sep 16 1991 macpattern13.hqx FILE -rwxr--r-- 97307 Sep 16 1991 macpattern2.hqx FILE -rwxr--r-- 35639 Sep 16 1991 macpattern3.hqx Host fly.bio.indiana.edu Location: /molbio/mac FILE -rw-r--r-- 1413 May 14 1991 macpattern.readme FILE -rw-r--r-- 228584 Jul 15 1991 macpattern13.hqx Host nic.funet.fi Location: /pub/sci/molbio/mac FILE -rw-rw-r-- 260963 Jun 23 1991 macpattern.hqx FILE -rw-rw-r-- 228146 Jun 27 1991 macpattern111.hqx FILE -rw-rw-r-- 188868 Jun 23 1991 macpattern123.hqx FILE -rw-rw-r-- 190886 Jun 23 1991 macpattern124.hqx FILE -rw-rw-r-- 228430 Jul 19 1991 macpattern13.hqx Host ra.nrl.navy.mil Location: /MacSciTech/biology FILE -rw-rw-rw- 228991 Dec 17 1991 MacPattern_15.hqx FILE -rw-rw-rw- 1688 Dec 17 1991 MacPattern_15.readme FILE -rw-rw-rw- 191809 Jul 2 1991 macpattern.hqx From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!news.cs.indiana.edu!sdd.hp.com!swrinde!gatech!darwin.sura.net!Sirius.dfn.de!chx400!urz.unibas.ch!bioftp.unibas.ch!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: EMBL CD-ROM goes double Message-ID: <1992Sep25.195242.48245@embl-heidelberg.de> Date: 25 Sep 92 18:52:42 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 28 The September 1992 issue of the EMBL CD-ROM will consist of two disks for the first time. We have arranged directories and files so that typical things can still be comfortably performed if you just have one CD-ROM drive. However, those people who use the EMBL CD-ROM on file servers may need this advance warning to rearrange their activity. Existing or prospective subscribers for the 1992/3 susbcription period need do nothing extra - the prices are the same - you will get both disks together. We expect to distribute this issue in 7-10 days. On volume 1, we include: - EMBL and Swiss-Prot in their flat-file distribution format - the MS-DOS and Mac query retrieval software and indices (which operate on the above flat-files) - related databases, particularly those with cross-references to/from the sequence databases (eg EPD, ECD, Prosite, Enzyme, REBASE) On volume 2, we include: - EMBL and Swiss-Prot in a 'FASTA' format, for use with Bill Pearson's FASTA for Mac or PC. - EMBLSCAN PC program and indices for fast lookup for very similar sequences in the EMBL nucleotide database. - a whole host of other molecular biology databases (eg TFD, FlyBase, Kabat, Berlin RNA database, RLDB, Seqanalref, tRNA, BLOCKS) Regards, Peter Stoehr EMBL Data Library From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!daresbury!bioftp.unibas.ch!embl-heidelberg.de!rainer-mac.embl-heidelberg.de!user From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs) Newsgroups: bionet.molbio.embldatabank Subject: Re: ftp at ftp.embl-heidelberg.de Message-ID: Date: 25 Sep 92 07:25:00 GMT References: <19pls2INNi56@grasp1.univ-lyon1.fr> Followup-To: bionet.molbio.embldatabank Organization: EMBL Data Library Lines: 17 Nntp-Posting-Host: rainer-mac.embl-heidelberg.de In article <19pls2INNi56@grasp1.univ-lyon1.fr>, Yvan Rahbe wrote: > > I would like to get MacPattern at the embl ftp site, and I have problem > in getteing reasonable access time to this server (camparatively to any > other server). I am using Fetch. Is there a reason for this ? The simple reason is that the German networks and their connection to the international Internet are not very effective, especially for generators of huge amounts of traffic such as EMBL. We are very actively investigating different approaches to improve this unsatisfactory situation. Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!daresbury!news From: karabinos@exmed1.dnet.gwdg.de ("EXMED1::KARABINOS") Newsgroups: bionet.molbio.embldatabank Subject: bionet-news Message-ID: <1992Sep24.213927.11686@gserv1.dl.ac.uk> Date: 24 Sep 92 21:29:36 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 1 Original-To: embl-db@uk.ac.daresbury sub bionet-news.bionet.molbio.embldatabank From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!rpi!ghost.dsi.unimi.it!univ-lyon1.fr!bio2.insa-lyon.fr!rahbe From: rahbe@jouy.inra.fr (Yvan Rahbe) Newsgroups: bionet.molbio.embldatabank Subject: ftp at ftp.embl-heidelberg.de Message-ID: <19pls2INNi56@grasp1.univ-lyon1.fr> Date: 23 Sep 92 11:53:38 GMT Organization: INRA -French Agronomic Research Institute- Lines: 14 NNTP-Posting-Host: bio2.insa-lyon.fr X-UserAgent: Nuntius v1.1.1d9 X-XXMessage-ID: X-XXDate: Wed, 23 Sep 92 13:54:49 GMT I would like to get MacPattern at the embl ftp site, and I have problem in getteing reasonable access time to this server (camparatively to any other server). I am using Fetch. Is there a reason for this ? Thanks ######################################################## # Yvan Rahbe phone: +33 - 72 43 83 56 # # INRA - INSA fax: +33 - 72 43 85 11 # # Biologie 406 internet: rahbe@lyon.inra.fr # # 20, av. A. Einstein =rahbe@jouy.inra.fr # # 69621 Villeurbanne cedex # # France United Europe # ######################################################## From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!daresbury!news From: dddzeij@nl.ruu.cc (van der Zeijst) Newsgroups: bionet.molbio.embldatabank Subject: no subject (file transmission) Message-ID: <1992Sep2.130815.10993@gserv1.dl.ac.uk> Date: 2 Sep 92 13:07:56 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 13 Original-To: embl-db@uk.ac.daresbury X-Mailer: ELM [version 2.3 PL11] Dear colleagues, We consulted accession number M84761, referred to by Amy et al. (PNAS 89, 1992, 1105-1108), who describe the sequence of the gene of rat fatty acid synthase. However, this number belongs to entry RNTHYBS, dealing with another gene (although Amy et al. are cited!). Could you advise us on how to retrieve the sequence of the gene for rat fatty acid synthase from the data base? Thank you very much in advance. Sincerely yours, Dr. J.A. Lenstra and Dr. J.J. Batenburg From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!WELCHGATE.WELCH.JHU.EDU!danj From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson x-8453) Newsgroups: bionet.molbio.embldatabank Subject: Re: How to retrieve sequences from EMBL and Genbank Message-ID: <9209021444.AA08524@welchgate.welch.jhu.edu> Date: 2 Sep 92 14:44:51 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 25 J.A. Lenstra and J.J. Batenburg write: >(....) >Could you advise us on how to retrieve the >sequence of the gene for rat fatty acid synthase from the data base? >Thank you very much in advance. I have sent the 4 sequences in Genbank which pertain to rat fatty acid synthase to them. There are several ways that you can access this data. You can use Gopher to retrieve them from fly.bio.indiana.edu (port 70) for genbank and bioftp.unibas.ch (port 70) for EMBL (if you don't know what gopher is let me know and I`ll send you some information). You can also telnet to genbank.bio.net and login as genbank, password is 4nigms and use the online IRX system to search for them (unfortunately this system will end at the end of this month). You can also use the mailserver search and retrieval at NCBI or EMBL (again I'll send you info if you haven't heard about this). Best of luck, Dan Jacobson From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!ARBO.MICROBIOL.UWA.EDU.AU!robert From: robert@ARBO.MICROBIOL.UWA.EDU.AU (Robert Coelen) Newsgroups: bionet.molbio.embldatabank Subject: (none) Message-ID: <46591.robert@arbo.microbiol.uwa.edu.au> Date: 24 Aug 92 18:56:30 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 1 help From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!WELCHGATE.WELCH.JHU.EDU!danj From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson x-8453) Newsgroups: bionet.molbio.embldatabank Subject: Sequence retrieval Message-ID: <9209021623.AA14466@welchgate.welch.jhu.edu> Date: 2 Sep 92 16:23:13 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 19 Hmm, seems that I forgot to include the PIR mailserver in my list of ways to access sequences. The following search would retrieve the desired sequences from the PIR mailserver. USE BASES EMBL+EMBLSUP+GBNEW QUERY TITLE FATTY ACID SYNTHASE SPECIES RAT GET ALL END QUERY Kudos go to John Garavelli for jogging my (failing) memory cells. Dan Jacobson From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!daresbury!bioftp.unibas.ch!embl-heidelberg.de!hazledine From: hazledine@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: 1992/93: Products, Services and Order Form Message-ID: <1992Jul20.170129.48213@embl-heidelberg.de> Date: 20 Jul 92 16:01:29 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 487 Here is a copy of our 1992/93 subscription order form, together with a description of the various products and services offered by the Data Library. These documents were recently posted to everyone on our mailing list. We would in particular like to draw your attention to a new data distribution format which we plan to begin offerring during the course of 1992/93, namely a relational table dump from our nucleotide sequence database. If you are interested in this format then do please contact the Data Library for further details, enclosing your postal address so that we can send documentation to you. We can be contacted as shown below: The EMBL Data Library Postfach 10.2209, Meyerhofstrasse 1, D-6900 Heidelberg, Germany. E-mail: DataLib@EMBL-Heidelberg.DE Fax: +49 6221 387519 Products and Services available from the EMBL Data Library. ----------------------------------------------------------- Contents * EMBL Databases on CD-ROM * EMBL Databases on Magnetic Tape * EMBL Network File Server * Summary of Available Databases * EMBnet: European Molecular Biology Network * Mail-Quicksearch and Mail-FastA * Sequence Data Submission * Database Subscription Form Subscriptions To RENEW YOUR SUBSCRIPTION, please fill in the form at the end of this package and return it to us. PLEASE NOTE that we offer to supply products by courier - costs borne by the subscriber. Also we now provide a faciltiy for automatic subscription renewal from year to year. A NEW FEATURE to be provided during the course of 1992 will be the availability of each quarterly release as a table dump from a relational schema, suitable for loading into any RDBMS. Please contact us if you wish to know more about this feature. May 1992 EMBL Databases on CD-ROM ------------------------ The following are available on CD-ROM: ------------------------------------------------------------------------------ EMBL NUCLEOTIDE Nucleotide sequence data, indices and documentation. SEQUENCE DATABASE ------------------------------------------------------------------------------ SWISS-PROT Protein sequence data, indices and documentation. DATABASE ------------------------------------------------------------------------------ RELATED DATABASES Several related databases are distributed as supplied by their authors. In cooperation with Nucleic Acids Research, we include databases published in their annual 'Sequence Supplement'. See the accompanying document 'Summary of Available Databases' for a full listing. ------------------------------------------------------------------------------ DATABASE QUERY/ MS-DOS software, CD-SEQ, is provided for query and RETRIEVAL retrieval of data from both the sequence databases on the CD-ROM allowing access by entry name, accession number, citation, author name, taxonomy, feature key, free text, database cross-reference and date. New Macintosh software, EMBL-Search, is provided to access the sequence databases via binary indices on the CD-ROM ------------------------------------------------------------------------------ SEQUENCE Sequence databases are provided in NBRF format for use SIMILARITY with software such as FASTA on Macintosh or MS-DOS systems. SEARCHING MS-DOS software, EMBLScan, is provided for rapid searching of the nucleotide database for very similar sequences. ------------------------------------------------------------------------------ INDICES A set of binary index files is provided which can be used by software to access rapidly the sequence databases on CD-ROM by, for example, entryname, accession number, free text, keywords, author names and taxonomy. ------------------------------------------------------------------------------ The CD-ROM is structured according to the ISO standard 9660 format. FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 EMBL Databases on Magnetic Tape ------------------------------- The EMBL databases are available on magnetic tape in a choice of medium and format making them usable on a range of computer systems. The options available are detailed on the Subscription Form. An EMBL Nucleotide Sequence subscription on magnetic tape includes: ------------------------------------------------------------------------------ EMBL NUCLEOTIDE Nucleotide sequence data, indices and documentation. SEQUENCE DATABASE ------------------------------------------------------------------------------ RELATED DATABASES Eukaryotic Promotor database (EPD) E. coli database (ECD) Restriction Enzyme database (REBASE) ------------------------------------------------------------------------------ A SWISS-PROT subscription on magnetic tape includes: ------------------------------------------------------------------------------ SWISS-PROT Protein sequence data, indices and documentation. DATABASE ------------------------------------------------------------------------------ RELATED DATABASES Prosite pattern database Enzyme nomenclature database. ------------------------------------------------------------------------------ FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 EMBL Network File Server ------------------------ The EMBL Network File Server is a facility enabling remote users to request files from EMBL via electronic mail. Information Accessible ------------------------------------------------------------------------------ * The EMBL Nucleotide Sequence Database (continuously updated with data from EMBL and GenBank & DDBJ) ------------------------------------------------------------------------------ * The SWISS-PROT Protein Sequence Database (including updates) ------------------------------------------------------------------------------ * The Brookhaven Protein Data Bank (and other structure data) ------------------------------------------------------------------------------ * Databases like E. coli database (ECD), eukaryotic promotor database (EPD), restriction enzyme database (REBASE), protein pattern database (Prosite) ------------------------------------------------------------------------------ * Free molecular biology software for MS-DOS, Apple Macintosh,VAX/VMS and UNIX. ------------------------------------------------------------------------------ * General documentation (like subscription and submission information) ------------------------------------------------------------------------------ Commands The file server is used by sending commands within electronic mail to the following Internet address: NetServ@EMBL-Heidelberg.DE. Requested files are returned automatically. The mail you send to the file server should contain one file server command per line. The best command to start with is:- HELP In response, the file server provides further documentation on how to proceed. FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 Summary of Available Databases ------------------------------ -------------------------------------------------------------------------------- Ref. Mag.Tape CD-ROM Server EMBL Nucleotide sequence database (1) * * * SWISS-PROT Protein sequence database (2) * * * ENZYME Database of EC nomenclature (3) * * * ECD E. coli map database (4) * * * EPD Eukaryotic promoter database (5) * * * FLYBASE Drosophila genetic map database (6) * * * PROSITE Protein pattern database (7) * * * REBASE Restriction enzyme database (8) * * * BERLIN 5S rRNA sequences (9) * * CUTG Codon usage tabulated from GenBank (10) * * HAEMB Haemophilia B database of mutations (11) * * METHYL Site specific methylation (12) * * RRNA Small subunit rRNA sequences (13) * * SMALLRNA Small RNA sequences (14) * * TFD Transcription factor database (15) * * TRNA tRNA sequences (16) * * 3D_ALI Sequence alignments based on structure superposition (17) * ALU ALU sequences and alignments (18) * DSSP Secondary structure digests of PDB files (19) * HSSP Homology-derived protein structures (20) * LIMB Listing of mol. biology databases (21) * PDB Brookhaven protein 3D structures (22) * SEQANALREF Articles dealing with sequence analysis (23) * -------------------------------------------------------------------------------- 1.Stoehr,P.J. and Cameron,G.N. (1991) Nucl. Acids Res., 19, 2227-2230. 2.Bairoch,A. and Boeckmann,B. (1991) Nucl. Acids Res., 19, 2247-2249. 3.Bairoch,A. (1990) University of Geneva, Geneva. 4.Krger,M., Wahl,R. and Rice,P. (1991) Nucl. Acids Res., 19, 2023-2043. 5.Bucher,P. and Trifonov,E.N. (1986) Nucl. Acids Res., 14, 10009-10026. 6.Ashburner,M. (1990) University of Cambridge, Cambridge. 7.Bairoch,A. (1991) Nucl. Acids Res. , 19, 2241-2245. 8.Roberts,R.J. (1985) Nucl. Acids Res., 13, r165-r200. 9.Specht,T., Wolters,J. and Erdmann,V.A. (1991) Nucl. Acids Res., 19, 2189-2191. 10.Wada,K., Wada,Y., Doi,H., Ishibashi,F., Gojobori,T. and Ikemura,T. (1991) Nucl. Acids Res.., 19, 1981-1986. 11.Giannelli,F., Green,P.M., High,K.A., Sommer,S., Lillicrap,D.P., Ludwig, M., Olek,K., Reitsma,P.H., Goosens,M., Yoshioka,A. and Brownlee,G.G. (1991) Nucl. Acids Res., 19, 2193-2220. 12.Nelson,M. and McClelland,M. (1991) Nucl. Acids Res., 19, 2045-2071. 13.Neefs,J.-M., Van de Peer,Y., De Rijk,P. Goris,A. and De Wachter,R. (1991) Nucl. Acids Res., 19, 1987-2015. 14.Gupta,S. and Reddy,R. (1991) Nucl. Acids Res., 19, 2073-2075. 15.Ghosh,D. (1990) Nucl. Acids Res., 18, 1749-1756. 16.Sprinzl,M, Dank,N., Nock,S. and Schoen A. (1991) Nuc.Acids Res.,19,2127-2171. 17.Pascarella,P. and Argos,P. (1992), in press. 18.Jurka,J. and Smith,T. (1988) Proc. Natl. Acad. Sci. U.S.A., 85, 74775-74778. 19.Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637 20.Sander,C. and Schneider,R. (1991) Proteins 9, 56-68. 21.Lawton,J.R.,Martinez,F.A. and Burks,C. (1989)Nucl.Acids Res., 17, 5885-5899. 22.Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F., Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) J. Mol. Biol., 112, 535-542. 23.Bairoch, A. (1991) University of Geneva, Geneva. May 1992 EMBnet : European Molecular Biology Network ------------------------------------------- Research in molecular biology and biotechnology requires computerised access to data including genetic sequences of proteins and nucleic acids, structures of biological macromolecules, human genome maps, genetic diseases, microbial strains, hybridomas, restriction enzymes, cloning vectors, industrial enzymes, taxonomic classification, toxicological data, and biomedical abstracts. EMBnet EMBnet is a collaborative initiative promoting access to information resources of importance to the European molecular biology and biotechnology research community. The computer network is based on nodes in European states providing biocomputing services for their academic and commercial users. Other nodes are involved as hosts of databases, specialised facilities or biocomputing research. Activities currently include: * daily distribution of new sequence data from EMBL Data Library to EMBnet national nodes, and then on to end-users. * on-line services with access to databases and analysis software * training On-line Access to the EMBL Nucleotide Sequence Database: The following EMBnet national nodes maintain daily-updated copies of the EMBL nucleotide sequence database for on-line access within their country. -------------------------------------------------------------------------------- Denmark: France: Germany: Greece: BIOBASE, CITI2, Paris. DKFZ, IMBB, Aarhus. Heidelberg. Heraklion. -------------------------------------------------------------------------------- Israel: Italy: Netherlands: Norway: Weizmann CNR Bari. CAOS/CAMM Biotechnology Institute, Centre, Centre of Oslo. Rehovot. Nijmegen. -------------------------------------------------------------------------------- Spain: Sweden: Switzerland: UK: CNB, Madrid. Biomedical Biozentrum, Daresbury Lab. Centre, Basel. Warrington. Uppsala. -------------------------------------------------------------------------------- EMBnet has received financial support from the Commission of the European Communities (CEC) under the BRIDGE programme. FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 Mail-Quicksearch and Mail-FastA ------------------------------- Mail-Quicksearch and Mail-FastA are two services available on the EMBL computing system that allow external users to search the DNA and protein sequence databases, including the most recent entries, via electronic mail. -------------------------------------------------------------------------------- MAIL-QUICKSEARCH Mail-Quicksearch is based on the NewQuicksearch and Quickmatch programs written by Peter Rice at EMBL, which are extensions of the Quicksearch programs contained in the GCG software package. You can very quickly search the EMBL database for sequences very similar to your query sequence. In addition to all entries contained in the latest EMBL release, all new EMBL and GenBank entries created since then are also accessible. -------------------------------------------------------------------------------- MAIL-FASTA Mail-FastA is based on Bill Pearson's FastA program. It allows you to perform rapid but sensitive comparisons of protein or DNA sequences against the databases. The databases available for searching include EMBL, GenBank, SwissProt and PIR. All new EMBL and GenBank entries are also accessible as soon as created. -------------------------------------------------------------------------------- Access These services are provided free of charge, though users may have to meet some of the communication costs depending on the accounting system at their site. To use Mail-Quicksearch, send mail to QUICK@EMBL-Heidelberg.DE. To use Mail-FastA, send mail to FASTA@EMBL-Heidelberg.DE. The mail you send should contain your query sequence and commands to specify search parameters. By typing HELP on a line by itself you can have returned to you further documentation on how to proceed. You should find out locally how to send electronic mail on your own computer to the Internet addresses above, but the EMBL Data Library will help in case of difficulty. FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 Sequence data Submission ------------------------ The EMBL Data Library accepts sequence data submissions in the following ways: -------------------------------------------------------------------------------- AUTHORIN SOFTWARE The latest versions of Macintosh and MS-DOS Authorin software Package are available from the file server by mailing the appropriate command to NETSERV@EMBL-HEIDELBERG.DE Use any of the following commands: HELP software GET Mac_software:authorin.hqx GET DOS_software:authorin.uaa -------------------------------------------------------------------------------- SUBMISSION FORM One submission form should be used for each nucleotide and protein sequence. * A computer-readable copy of the submission form is included with each release of the sequence databases. * It is also available from the file server by sending the following command to NETSERV@EMBL-HEIDELBERG.DE GET DOC:datasub.txt * Printed copies of the submission form are published in the first issue each year of Nucleic Acids Resarch. They are also available on request from the Data Library. -------------------------------------------------------------------------------- DATA SUBMISSION by E-mail Send the completed form and appended sequence to : DATASUBS@EMBL-HEIDELBERG.DE ensuring data lines are no longer than 80 characters. by Post Send the sequence on MACINTOSH or IBM-PC COMPATIBLE DISKETTES together with the completed form either on the disk or as paper copy. Use the 'Save as text only' feature of your editor, to produce ASCII formatted data -------------------------------------------------------------------------------- FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 EMBL DATA LIBRARY SUBSCRIPTION FORM 1992/93 Subscription No: [ ] Please quote this, if given, in any correspondence. ------------------------------------------------------------------------------ Name: ------------------------------------------------------------------------------ Institute/Company: ------------------------------------------------------------------------------ Postal Address: | Invoice Address ( If not Postal Address | | | | | | | ------------------------------------------------------------------------------ Telephone: Telefax: ------------------------------------------------------------------------------ Email address: ------------------------------------------------------------------------------ CD-ROM RELEASES [ ] copies containing Release 32 & SWISSPROT Release 23 September 1992 [ ] Release 33 & SWISSPROT Release 24 December 1992 [ ] Release 34 & SWISSPROT Release 25 March 1993 [ ] Release 35 & SWISSPROT Release 26 June 1993 ------------------------------------------------------------------------------ MAGNETIC TAPE RELEASES EMBL NUCLEOTIDE SEQUENCE DATABASE SWISSPROT PROTEIN SEQUENCE DATABASE [ ] Release 32, September 1992 [ ] Release 24, November 1992 [ ] Release 33, December 1992 [ ] Release 25, February 1993 [ ] Release 34, March 1993 [ ] Release 26, May 1993 [ ] Release 35, June 1993 [ ] Release 27, August 1993 ------------------------------------------------------------------------------ TAPE FORMAT: Tape density will be 6250 bpi. Options * will be used for items left blank. Tape Medium: Tape blocksize: Tape Character Set: [* ] Unlabelled tape [* ] 8000 bytes [* ] ASCII [ ] ANSI labels [ ] 4000 bytes [ ] EBCDIC [ ] IBM labels [ ] bytes [ ] VMS Backup [ ] TK70 cartridge -------------------------------------------------------------------------------- SUBSCRIPTION CATEGORY [ ] Academic [ ] Commercial -------------------------------------------------------------------------------- COURIER DELIVERY [ ] Yes [ ] No -------------------------------------------------------------------------------- AUTOMATIC SUBSCRIPTION RENEWAL [ ] Yes [ ] No -------------------------------------------------------------------------------- Prices in DM per quarterly release: -------------------------------------------------------------------------------- SUBSCRIPTION CATEGORY | CDROM | Mag Tape ---------------------------------+-------------------+-------------------------- Academic - EMBL/ EC member state | 75.00 | 75.00 Academic - non-member state | 150.00 | 150.00 Commercial | 300.00 | 300.00 -------------------------------------------------------------------------------- From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!daresbury!bioftp.unibas.ch!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: Renewal of EMBL CD-ROM/tape subscriptions Message-ID: <1992Sep3.110655.48240@embl-heidelberg.de> Date: 3 Sep 92 10:06:55 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 16 Subscribers to EMBL CD-ROM's and magnetic tapes are reminded that September 1992 marks the beginning of a new subscription period. To renew subscriptions please return the subscription forms which were part of our May mail-shot. New forms can be sent via e-mail, post or fax on request or can be retrieved from the EMBL mail or FTP servers. 1- E-mail file server: send e-mail to NetServ@EMBL-Heidelberg.DE containing the line: GET DOC:ORDERFORM.TXT 2- Anonymous FTP : connect using FTP to FTP.EMBL-Heidelberg.DE and get the (ascii) file in /pub/doc/orderform.txt Regards, Peter Stoehr EMBL Data Library, Postfach 10.2209, 6900 Heidelberg, Germany. Tel: +49 6221 387258 E-mail: DataLib@EMBL-Heidelberg.DE Fax: +49 6221 387519 From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!uwm.edu!spool.mu.edu!uunet!mcsun!sun4nl!wn1.sci.kun.nl!camms4.caos.kun.nl!jackl From: jackl@camms4.caos.kun.nl (Jack Leunissen) Newsgroups: bionet.molbio.embldatabank Subject: Re: no subject (file transmission) Message-ID: Date: 18 Sep 92 14:46:47 GMT References: <1992Sep2.130815.10993@gserv1.dl.ac.uk> Sender: news@sci.kun.nl (NUnet News Owner) Distribution: bionet Organization: University of Nijmegen Lines: 43 Dr. J.A. Lenstra and Dr. J.J. Batenburg write: |> We consulted accession number M84761, referred to by Amy et al. |> (PNAS 89, 1992, 1105-1108), who describe the sequence of the gene of |> rat fatty acid synthase. |> However, this number belongs to entry RNTHYBS, dealing with another gene |> (although Amy et al. are cited!). Could you advise us on how to retrieve the |> sequence of the gene for rat fatty acid synthase from the data base? |> Thank you very much in advance. |> The sequence has been corrected, and is now available under the same accession number and EMBL db-code, in the daily updates from EMBL. The correction is marked 29-Aug-1992. In general, it can be found at the national nodes in EMBnet, which have a daily updated version of the sequence database(s). At the CAOS/CAMM Center, you can search the databases using XQS, issuing the commands: FIND FATTY ACID SYNTHASE SPECIES/CURRENT RATTUS This gives you the following hits: Rattus norvegicus (rat) EMNEW:RNFASF R. norvegicus FAS gene for fatty acid synthase EMNEW:RNTHYBS Rat fatty acid synthase gene, complete cds. EM_RO:RNFAACSY Rat gene for fatty acid synthase (promoter region, exons 1- 2) EM_RO:RNFAS Rat mRNA for fatty acid synthase (EC 2.3.1.85) EM_RO:RNFASA R.norvegicus fatty acid synthase mRNA, complete cds 1 species found Hope this helps, Rgrds, Jack +-------------------------------+-----------------------------------+ Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center Email: jackl@caos.caos.kun.nl | University of Nijmegen Tel. : +31 80 65 22 48 | Toernooiveld Fax : +31 80 65 29 77 | 6525 ED Nijmegen, The Netherlands +---------- CAOS/CAMM is the Dutch National Node in EMBnet ---------+ From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!EMBL-HEIDELBERG.DE!Rainer.Fuchs From: Rainer.Fuchs@EMBL-HEIDELBERG.DE ("Rainer Fuchs ", EMBL Data Library) Newsgroups: bionet.molbio.embldatabank Subject: French CEPH/Genethon cDNA project Message-ID: Date: 26 Jun 92 12:46:00 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 20 For your information: The first sequence data from the French Genexpress human cDNA sequencing program, one of the three scientific programs at Genethon*, have been incorporated into the international nucleotide sequence database this week. As the result of a collaboration between Genethon and the EMBL Data Library these sequences are processed automatically and enter the database immediately they are transmitted to EMBL. The partial sequences of these "transcribed sequence fragments" (a term the scientists involved find preferable to "ESTs") are derived by single reads of one strand of cDNA clones from human cell lines. About 1000 sequences arrived this week, and a constant flow of new data is expected for the future. Rainer Fuchs (the EMBL Data Library) Patricia Rodriguez-Tome (Genethon, Computer Center) Charles Auffray (Genethon/CNRS) Director of Genexpress program *Genethon is a pluridisciplinary multi-annual program initialized by CEPH, funded by AFM (Association Francaise contre les Myopathies) and sponsored by CNRS From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!EMBL-HEIDELBERG.DE!NETHELP From: NETHELP@EMBL-HEIDELBERG.DE Newsgroups: bionet.molbio.embldatabank Subject: EMBL File Server News, No. 8 June 25th 1992 Message-ID: <1114572D00213E25@EMBL-Heidelberg.DE> Date: 25 Jun 92 12:10:00 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 432 ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 8, June 25th 1992 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 6900 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Anonymous FTP server <3> Gopher server <4> Updates to data collections <5> Updates to software collection <6> Other updates <7> Summary of directories on the file server <8> Getting started ? <9> Network addresses at EMBL <10> Footnotes <1> Introduction ------------- The EMBL File Server is a facility available on the EMBL computing system for external users to request files by electronic mail or anonymous FTP. The service is free. <2> Anonymous FTP server -------------------- An anonymous FTP server is now operational at the internet address FTP.EMBL-Heidelberg.DE (192.54.41.33) Users should log in with the username "anonymous", and for the password give their e-mail address. The FTP archive currently contains molecular biology databases, free molecular biology software and other files similar to the facilities offered by the e-mail server (NetServ@EMBL-Heidelberg.DE). Weekly batches of additions to the EMBL nucleotide sequence database (data from EMBL/GenBank/DDBJ) are made available as compressed tar files in the directory: /pub/databases/embl/new Individual sequence database entries are not available via FTP: we recommend use of the e-mail server for this purpose. <3> Gopher server ------------- A gopher server is available as part of an experimental network of EMBnet gopher sites, providing access to the EMBL FTP archive and to other "Biogophers" in Europe, Israel and the USA. Gopher clients should connect to FTP.EMBL-Heidelberg.DE at port 70. Administrators of other Gopher servers may add the following link information: Name=EMBnet BioInformation Resource EMBL Type=1 Port=70 Path=1/ Host=ftp.embl-heidelberg.de <4> Updates to Data Collections ------------------------------------ Two new databases have been added to the file server recently: (a) The Reference Library Database system (RLDB) provided by Guenther Zehetner, Genome Analysis Laboratory, ICRF, London. E-mail server: directory RLDB Anonymous ftp: /pub/databases/rldb (b) A database of 3-D alignments (3D_ALI) provided by Stefan Pascarella and Pat Argos, EMBL. Pascarella S., Argos P. "A data bank merging related protein structures and sequences" Protein Engineering 5 (1) 121-137 (1992). E-mail server: directory 3D_ALI Anonymous ftp: /pub/databases/3d_ali <5> Updates to Software Collection ------------------------------ Here is a list of new (N) molecular biological programs or updates (U): The full path specifications for these files on the EMBL ftp server are shown in square brackets. DOS: ---- DNAFRAG.UUE (N) Measures molecule size of gel bands from standards (J. Nash) [/pub/software/dos/dnafrag.uue] GEL-JML.UAA (N) Calculation of DNA restriction fragment sizes (J.M. Lacroix) [/pub/software/dos/gel-jml.uaa and gel-jml.uab] GMD.TXT (N) Programs to assist in the design of genome mapping experiments (contig mapping) (Y. Fu) [/pub/software/dos/gmd.txt] MACAW103.UAA (N) Multiple sequence editor (G. Schuler) [/pub/software/dos/macaw103.uaa to macaw103.uac] MARKER.UUE (U) Creation of restriction fragments banding patterns and DNA length standards v1.1 (S. Rensing) [/pub/software/dos/marker.uue] MISMATCH.TXT (N) Selection of PCR designed mismatch primers (L.S. Davidow) [/pub/software/dos/mismatch.txt] NUMCLONE.UUE (N) Estimates the number of clones one has to screen from a genomic library in order to find a desired clone (J. Nash) [/pub/software/dos/numclone.uue] PRIMGEN.UUE (N) Oligonucleotide primer design by reverse-translation of amino acid sequences (J. Nash) [/pub/software/dos/primgen.uue] PRNTGL.UAA (U) Prints HGPL files on matrix of laser printer v1.18 (C. Ravitz) [/pub/software/dos/prntgl.uaa and prntgl.uab] SIM.UUE (U) Local similarity searching (G. Huang) [/pub/software/dos/sim.uue] SSCAN.UAA (U) Identification of eukaryotic signals in DNA sequences, v3.0 (D. Prestridge) [/pub/software/dos/sscan.uaa to scan.uad] Mac: ---- ALIGNER.HQX (N) Multiple sequence editor (D. Eernisse) [/pub/software/mac/aligner.hqx] AMPLIFY.HQX (N) Tools for PCR primer checks (B. Engels) [/pub/software/mac/amplify.hqx] DNAID.HQX (U) DNA sequence editor and analysis program v1.6 (F. Dardel) [/pub/software/mac/dnaid.hqx] EMBL-SEARCH.HQX (N) Database retrieval software for EMBL CD-ROM (R. Fuchs) [/pub/software/mac/embl-search.hqx] EMBL-SEARCH_SRC.HQX (N) Source code for EMBL-Search v2.0 [/pub/software/mac/embl-search_src.hqx] GBSEARCH.HQX (U) Tool to assist access to GenBank server (D. Gilbert) [/pub/software/mac/gbsearch.hqx] GENEWORKS_DEMO.HQX (N) Demo version of IG's sequence analysis package [/pub/software/mac/geneworks_demo.hqx] GENE_JOCKEY_DEMO.HQX (N) Demo version of Biosoft's sequence analysis package [/pub/software/mac/gene_jockey_demo.hqx] GMD.TXT (N) Programs to assist in the design of genome mapping experiments (contig mapping) (Y. Fu) [/pub/software/mac/gmd.txt] MACMIMIC_DEMO.HQX (N) Demo version of Instar's molecular modelling package [/pub/software/mac/macmimic_demo.hqx] MACMOLECULE.HQX (U) 3d models of biomolecules v1.7 (E. Myers) [/pub/software/mac/macmolecule.hqx] MACPATTERN.HQX (U) Protein pattern searching with Prosite, v1.6.2 (R. Fuchs) [/pub/software/mac/macpattern.hqx] MACSIGNALSCAN.HQX (N) Identification of eukaryotic signals in DNA sequences, v3.0 (D. Prestridge) [/pub/software/mac/macsignalscan.hqx] MACVECTOR_DEMO.HQX (N) Demo of IBI's sequence analysis package [/pub/software/mac/macvector_demo.hqx] SIGNALASE.HQX (N) Analysis of mammalian signal peptide sequences (N. Matei) [/pub/software/mac/signalase.hqx] UNIX: ----- BLAST.UAA (U) Fast sequence database searching [/pub/software/unix/blast.tar.Z] DFA.UAA (U) Required by BLAST.UAA [/pub/software/unix/dfa.tar.Z] FILTER.UAA (N) Set of programs for suboptimal alignments ans recognition of reliably aligned sequences (P. Argos) [/pub/software/unix/filter.tar.Z] GCI.UAA (N) A network server for interactive 3D graphics (G. Tuparev) [/pub/software/unix/gci.tar.Z] GISH.UUE (U) Required by BLAST.UAA [/pub/software/unix/gish.tar.Z] GMD.TXT (N) Programs to assist in the design of genome mapping experiments (contig mapping) (Y. Fu) [/pub/software/unix/gmd.txt] MAILFASTA.UUE (U) Script for using EMBL/GenBank Mail-FASTA servers v2.1 (T. deBoer) [/pub/software/unix/mailfasta.tar.Z] NCBI.UAA (U) Required by BLAST.UAA [/pub/software/unix/ncbi.tar.Z] PIMA.UAA (U) Pattern-induced multi-sequence alignments v1.22 (R.F. Smith) [/pub/software/unix/pima.tar.Z] PLSEARCH.UAA (U) Pattern detection in proteins v4.2 (R.F. Smith) [/pub/software/unix/plsearch.tar.Z] READSEQ.UUE (U) Sequence format conversion program, Apr 1992 (D. Gilbert) [/pub/software/unix/readseq.tar.Z] SIGSCAN.UAA (U) Identification of eukaryotic signals in DNA sequences, v3.0 (D. Prestridge) [/pub/software/unix/sigscan.tar.Z] SIM.UUE (U) Local similarity searching (G. Huang) [/pub/software/unix/sim.tar.Z] VAX: ---- BLASTMAIL.COM (N) DCL script for using GenBank's BLAST server (E.L. Sonnhammer) [/pub/software/vax/blastmail.com] FASTEMBL.COM (U) Script for using the EMBL Mail-Fasta server (for GCG 7), v 1.w (E. Sonnhammer) [/pub/software/vax/fastembl.com] FILTER.UAA (N) Set of programs for suboptimal alignments ans recognition of reliably aligned sequences (P. Argos) [/pub/software/vax/filter.uaa to filter.uac] GMD.TXT (N) Programs to assist in the design of genome mapping experiments (contig mapping) (Y. Fu) [/pub/software/vax/gmd.txt] INTERFACE.UUE (N) Pascal programming interface for GCG package (J. Prilusky) [/pub/software/vax/interface.uue] MALIGNED.UAA (U) Multiple sequence editor, v1.65b (S. Clark) [/pub/software/vax/maligned.uaa to maligned.uad] READSEQ.UAA (U) Sequence format conversion program, Apr 1992 (D. Gilbert) [/pub/software/vax/readseq.uaa and readseq.uab] SCRUTINE.UAA (U) Scrutineer, sequence database analysis, Jun 1992 (P. Sibbald) [/pub/softare/vax/scrutine.uaa] SIM.UUE (U) Local similarity searching (G. Huang) [/pub/software/vax/sim.uue] SSCAN.UAA (U) Identification of eukaryotic signals in DNA sequences, v3.0 (D. Prestridge) [/pub/software/vax/sscan.uaa to sscan.uac] <6> Other updates ------------- ALIGN directory: o DS10014.DAT - Alignment of exon 1 of the interphoto- receptor binding protein (IRBP) gene. Submitted by J. Stanhope, 4-Feb-1992. o DS10763.DAT - Alignment of duplicated gamme globin gene sequences from mammals. Submitted by W. Bailey, 24-Apr-1992. o DS10819.DAT - Alignment of potassium channel gene family. Submitted by M. Strong, 13-May-1992 o DS10830.DAT - Alignment of potassium channel genes, Shaw related gene family. Submitted by M. Strong, 14-May-1992 o DS10831.DAT - Alignment of S4 segment of Na+,Ca++, and K+ ion channel genes. Submitted by M. Strong, 14-May-1992 o DS10832.DAT - Alignment of potassium channel genes, Shaker related gene family. Submitted by M. Strong, 13-May-1992 o DS10833.DAT - Alignment of sodium channel gene family. Submitted by M. Strong, 13-May-1992 <7> Summary of directories on the file server --------------------------------------- Anonymous ftp NetServ -------------- --------- EMBL Nucleotide Sequence Database /pub/databases/embl NUC (Rel. 31, Jun 92 + updates) Eukaryotic Promotor Database /pub/databases/epd EPD (Rel. 31, May 92) SwissProt Protein Sequence Database /pub/databases/swissprot PROT (Rel. 22, May 92 + updates) Prosite pattern database /pub/databases/prosite PROSITE (Rel. 9.00, Jun 92) ENZYME database /pub/databases/enzyme ENZYME (Rel. 9.00, May 92) Brookhaven Protein Databank not available PROTEINDATA (Rel. 58, Oct 91) REBASE, Restriction Enzyme Database /pub/databases/rebase REBASE (Rel. 9206, Jun 92) tRNA sequence and gene sequence db /pub/databases/trna TRNA (1991) TFD, Transcription Factor Database /pub/databases/tfd TFD (Ver 4.3, Mar 92) ECD, E.coli Database /pub/databases/ecd ECD (Rel. 11, Jun 92) FLYBASE, Drosophila Genetic Map db /pub/databases/flybase FLYBASE (9206, 1-Jun-1992) LiMB, Listing of Mol. Biol. db's /pub/databases/limb LIMB (Rel. 2.0) SEQANALREF, Seq. analysis refs /pub/databases/reflist REFLIST (Rel. 28, Jun 92) FANS_REF, Functional analysis refs /pub/databases/reflist REFLIST (Rel. 3.4, Apr 91) Alu sequence database and alignment /pub/databases/alu ALU Haemophilia B database /pub/databases/haemb HAEMB (Dec 1991) Compilation of small RNA sequences /pub/databases/smallrna SMALLRNA (Oct 91) Berlin Databank of 5S rRNA and /pub/databases/berlin BERLIN 5S rRNA gene sequences (1991) Compilation of small ribosomal /pub/databases/rrna RRNA subunit RNA sequences (1991) CUTG, codon usage /pub/databases/cutg CUTG tabulated from GenBank rel. 69 3D_Ali, 3D alignment database /pub/databases/3d_ali 3D_ALI (March 1992) RLDB, Reference Library Database /pub/databases/rldb RLDB (April 1992) Software: Software for MS-DOS computers /pub/software/dos DOS_SOFTWARE Software for Apple Macintosh /pub/software/mac MAC_SOFTWARE Software for UNIX /pub/software/unix UNIX_SOFTWARE Software for VAX/VMS /pub/software/vax VAX_SOFTWARE Other software /pub/software/misc MISC_SOFTWARE Miscellaneous: Technical documents, submission and /pub/doc DOC order forms, etc. Multiple DNA sequence alignments /pub/databases/embl/align ALIGN and consensus sequences Codon Usage tables /pub/databases/codonusage CODONUSAGE <8> Getting Started ? ----------------- For initial information, send standard electronic mail to the address: NetServ@EMBL-Heidelberg.DE containing just the word HELP on a line by itself. To use the anonymous ftp server, connect to the internet address FTP.EMBL-Heidelberg.DE using the username "anonymous" (without the quotes !) and giving your e-mail address as the password. Look in the directory /pub/help for various help files. <9> Network addresses at EMBL ------------------------- EMBL File Server (e-mail requests) NetServ@EMBL-Heidelberg.DE FASTA e-mail server FASTA@EMBL-Heidelberg.DE Quicksearch e-mail server Quick@EMBL-Heidelberg.DE Anonymous FTP FTP.EMBL-Heidelberg.DE Problems, feedback (human contact) NetHelp@EMBL-Heidelberg.DE EMBL Data Library enquiries DataLib@EMBL-Heidelberg.DE EMBL Data Library sequence submissions DataSubs@EMBL-Heidelberg.DE Software submissions and problems Software@EMBL-Heidelberg.DE <10> Footnotes --------- REMINDER: EMBL has withdrawn from the BITNET/EARN computer network. Use only the Internet address, eg NetServ@EMBL-Heidelberg.DE The old address, eg Netserv@EMBL.bitnet, is terminated. The EMBL File Server Newsletter summarises changes to the EMBL File Server. This newsletter and older issues are available from the mail server (eg. GET DOC:EMBL_Server_News.7), or via anonymous ftp in the directory /pub/doc From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!daresbury!news From: maha%maha@it.cnr.na.maha (Veeramani Maharajan) Newsgroups: bionet.molbio.embldatabank Subject: None Message-ID: <1992Jul13.101815.17535@gserv1.dl.ac.uk> Date: 13 Jul 92 17:20:17 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 5 Original-To: embl-db@uk.ac.daresbury X-Mailer: LeeMail 1.2 Please inform if the cDNA sequence for Buffalo (Bubabul bubalis or related species) is available in your data bank. If possible please send details: sequence, authors, etc. Thanking you V. Maharajan From owner-embldatabank@net.bio.net Sun Sep 27 23:00:00 1992 Path: bionet!EMBL-HEIDELBERG.DE!David.Hazledine From: David.Hazledine@EMBL-HEIDELBERG.DE (David Hazledine) Newsgroups: bionet.molbio.embldatabank Subject: EMBL Data Library Products and Services, 1992/93 Message-ID: Date: 6 Jul 92 15:35:00 GMT Sender: daemon@genbank.bio.net Distribution: bionet Lines: 484 EMBL Data Library Products and Services, 1992/93 ================================================ Here is a copy of the material concerning services and subscriptions to the EMBL Data Library for 1992/93, which was recently posted to everyone on our mailing list. If you know of someone who might be interested in this, and who may not see it on this bulletin board, then please forward it on to them. Thank you. We would in particular like to draw your attention to the new data distribution format we plan to introduce in the course of the coming 12 months (i.e. our nucleotide sequence database in the form of a text file dump of tables from a relational schema; if you would like more details then please contact us at Datalib@EMBL-Heidelberg.DE with your fax number or postal address). Products and Services available from the EMBL Data Library. ----------------------------------------------------------- Contents * EMBL Databases on CD-ROM * EMBL Databases on Magnetic Tape * EMBL Network File Server * Summary of Available Databases * EMBnet: European Molecular Biology Network * Mail-Quicksearch and Mail-FastA * Sequence Data Submission * Database Subscription Form Subscriptions To RENEW YOUR SUBSCRIPTION, please fill in the form at the end of this package and return it to us. PLEASE NOTE that we offer to supply products by courier - costs borne by the subscriber. Also we now provide a faciltiy for automatic subscription renewal from year to year. A NEW FEATURE to be provided during the course of 1992 will be the availability of each quarterly release as a table dump from a relational schema, suitable for loading into any RDBMS. Please contact us if you wish to know more about this feature. May 1992 EMBL Databases on CD-ROM ------------------------ The following are available on CD-ROM: ------------------------------------------------------------------------------ EMBL NUCLEOTIDE Nucleotide sequence data, indices and documentation. SEQUENCE DATABASE ------------------------------------------------------------------------------ SWISS-PROT Protein sequence data, indices and documentation. DATABASE ------------------------------------------------------------------------------ RELATED DATABASES Several related databases are distributed as supplied by their authors. In cooperation with Nucleic Acids Research, we include databases published in their annual 'Sequence Supplement'. See the accompanying document 'Summary of Available Databases' for a full listing. ------------------------------------------------------------------------------ DATABASE QUERY/ MS-DOS software, CD-SEQ, is provided for query and RETRIEVAL retrieval of data from both the sequence databases on the CD-ROM allowing access by entry name, accession number, citation, author name, taxonomy, feature key, free text, database cross-reference and date. New Macintosh software, EMBL-Search, is provided to access the sequence databases via binary indices on the CD-ROM ------------------------------------------------------------------------------ SEQUENCE Sequence databases are provided in NBRF format for use SIMILARITY with software such as FASTA on Macintosh or MS-DOS systems. SEARCHING MS-DOS software, EMBLScan, is provided for rapid searching of the nucleotide database for very similar sequences. ------------------------------------------------------------------------------ INDICES A set of binary index files is provided which can be used by software to access rapidly the sequence databases on CD-ROM by, for example, entryname, accession number, free text, keywords, author names and taxonomy. ------------------------------------------------------------------------------ The CD-ROM is structured according to the ISO standard 9660 format. FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 EMBL Databases on Magnetic Tape ------------------------------- The EMBL databases are available on magnetic tape in a choice of medium and format making them usable on a range of computer systems. The options available are detailed on the Subscription Form. An EMBL Nucleotide Sequence subscription on magnetic tape includes: ------------------------------------------------------------------------------ EMBL NUCLEOTIDE Nucleotide sequence data, indices and documentation. SEQUENCE DATABASE ------------------------------------------------------------------------------ RELATED DATABASES Eukaryotic Promotor database (EPD) E. coli database (ECD) Restriction Enzyme database (REBASE) ------------------------------------------------------------------------------ A SWISS-PROT subscription on magnetic tape includes: ------------------------------------------------------------------------------ SWISS-PROT Protein sequence data, indices and documentation. DATABASE ------------------------------------------------------------------------------ RELATED DATABASES Prosite pattern database Enzyme nomenclature database. ------------------------------------------------------------------------------ FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 EMBL Network File Server ------------------------ The EMBL Network File Server is a facility enabling remote users to request files from EMBL via electronic mail. Information Accessible ------------------------------------------------------------------------------ * The EMBL Nucleotide Sequence Database (continuously updated with data from EMBL and GenBank & DDBJ) ------------------------------------------------------------------------------ * The SWISS-PROT Protein Sequence Database (including updates) ------------------------------------------------------------------------------ * The Brookhaven Protein Data Bank (and other structure data) ------------------------------------------------------------------------------ * Databases like E. coli database (ECD), eukaryotic promotor database (EPD), restriction enzyme database (REBASE), protein pattern database (Prosite) ------------------------------------------------------------------------------ * Free molecular biology software for MS-DOS, Apple Macintosh,VAX/VMS and UNIX. ------------------------------------------------------------------------------ * General documentation (like subscription and submission information) ------------------------------------------------------------------------------ Commands The file server is used by sending commands within electronic mail to the following Internet address: NetServ@EMBL-Heidelberg.DE. Requested files are returned automatically. The mail you send to the file server should contain one file server command per line. The best command to start with is:- HELP In response, the file server provides further documentation on how to proceed. FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 Summary of Available Databases ------------------------------ -------------------------------------------------------------------------------- Ref. Mag.Tape CD-ROM Server EMBL Nucleotide sequence database (1) * * * SWISS-PROT Protein sequence database (2) * * * ENZYME Database of EC nomenclature (3) * * * ECD E. coli map database (4) * * * EPD Eukaryotic promoter database (5) * * * FLYBASE Drosophila genetic map database (6) * * * PROSITE Protein pattern database (7) * * * REBASE Restriction enzyme database (8) * * * BERLIN 5S rRNA sequences (9) * * CUTG Codon usage tabulated from GenBank (10) * * HAEMB Haemophilia B database of mutations (11) * * METHYL Site specific methylation (12) * * RRNA Small subunit rRNA sequences (13) * * SMALLRNA Small RNA sequences (14) * * TFD Transcription factor database (15) * * TRNA tRNA sequences (16) * * 3D_ALI Sequence alignments based on structure superposition (17) * ALU ALU sequences and alignments (18) * DSSP Secondary structure digests of PDB files (19) * HSSP Homology-derived protein structures (20) * LIMB Listing of mol. biology databases (21) * PDB Brookhaven protein 3D structures (22) * SEQANALREF Articles dealing with sequence analysis (23) * -------------------------------------------------------------------------------- 1.Stoehr,P.J. and Cameron,G.N. (1991) Nucl. Acids Res., 19, 2227-2230. 2.Bairoch,A. and Boeckmann,B. (1991) Nucl. Acids Res., 19, 2247-2249. 3.Bairoch,A. (1990) University of Geneva, Geneva. 4.Krger,M., Wahl,R. and Rice,P. (1991) Nucl. Acids Res., 19, 2023-2043. 5.Bucher,P. and Trifonov,E.N. (1986) Nucl. Acids Res., 14, 10009-10026. 6.Ashburner,M. (1990) University of Cambridge, Cambridge. 7.Bairoch,A. (1991) Nucl. Acids Res. , 19, 2241-2245. 8.Roberts,R.J. (1985) Nucl. Acids Res., 13, r165-r200. 9.Specht,T., Wolters,J. and Erdmann,V.A. (1991) Nucl. Acids Res., 19, 2189-2191. 10.Wada,K., Wada,Y., Doi,H., Ishibashi,F., Gojobori,T. and Ikemura,T. (1991) Nucl. Acids Res.., 19, 1981-1986. 11.Giannelli,F., Green,P.M., High,K.A., Sommer,S., Lillicrap,D.P., Ludwig, M., Olek,K., Reitsma,P.H., Goosens,M., Yoshioka,A. and Brownlee,G.G. (1991) Nucl. Acids Res., 19, 2193-2220. 12.Nelson,M. and McClelland,M. (1991) Nucl. Acids Res., 19, 2045-2071. 13.Neefs,J.-M., Van de Peer,Y., De Rijk,P. Goris,A. and De Wachter,R. (1991) Nucl. Acids Res., 19, 1987-2015. 14.Gupta,S. and Reddy,R. (1991) Nucl. Acids Res., 19, 2073-2075. 15.Ghosh,D. (1990) Nucl. Acids Res., 18, 1749-1756. 16.Sprinzl,M, Dank,N., Nock,S. and Schoen A. (1991) Nuc.Acids Res.,19,2127-2171. 17.Pascarella,P. and Argos,P. (1992), in press. 18.Jurka,J. and Smith,T. (1988) Proc. Natl. Acad. Sci. U.S.A., 85, 74775-74778. 19.Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637 20.Sander,C. and Schneider,R. (1991) Proteins 9, 56-68. 21.Lawton,J.R.,Martinez,F.A. and Burks,C. (1989)Nucl.Acids Res., 17, 5885-5899. 22.Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F., Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) J. Mol. Biol., 112, 535-542. 23.Bairoch, A. (1991) University of Geneva, Geneva. May 1992 EMBnet : European Molecular Biology Network ------------------------------------------- Research in molecular biology and biotechnology requires computerised access to data including genetic sequences of proteins and nucleic acids, structures of biological macromolecules, human genome maps, genetic diseases, microbial strains, hybridomas, restriction enzymes, cloning vectors, industrial enzymes, taxonomic classification, toxicological data, and biomedical abstracts. EMBnet EMBnet is a collaborative initiative promoting access to information resources of importance to the European molecular biology and biotechnology research community. The computer network is based on nodes in European states providing biocomputing services for their academic and commercial users. Other nodes are involved as hosts of databases, specialised facilities or biocomputing research. Activities currently include: * daily distribution of new sequence data from EMBL Data Library to EMBnet national nodes, and then on to end-users. * on-line services with access to databases and analysis software * training On-line Access to the EMBL Nucleotide Sequence Database: The following EMBnet national nodes maintain daily-updated copies of the EMBL nucleotide sequence database for on-line access within their country. -------------------------------------------------------------------------------- Denmark: France: Germany: Greece: BIOBASE, CITI2, Paris. DKFZ, IMBB, Aarhus. Heidelberg. Heraklion. -------------------------------------------------------------------------------- Israel: Italy: Netherlands: Norway: Weizmann CNR Bari. CAOS/CAMM Biotechnology Institute, Centre, Centre of Oslo. Rehovot. Nijmegen. -------------------------------------------------------------------------------- Spain: Sweden: Switzerland: UK: CNB, Madrid. Biomedical Biozentrum, Daresbury Lab. Centre, Basel. Warrington. Uppsala. -------------------------------------------------------------------------------- EMBnet has received financial support from the Commission of the European Communities (CEC) under the BRIDGE programme. FURTHER INFORMATION: The EMBL Data Library E-mail:DataLib@EMBL-Heidelberg.DE Postfach 10.2209, Meyerhofstrasse 1, Fax: +49 6221 387519 D-6900 Heidelberg, Germany. Tel: +49 6221 387258 May 1992 Mail-Quicksearch and Mail-FastA ------------------------------- Mail-Quicksearch and Mail-FastA are two services available on the EMBL computing system that allow external users to search the DNA and protein sequence databases, including the most recent entries, via electronic mail. -------------------------------------------------------------------------------- MAIL-QUICKSEARCH Mail-Quicksearch is based on the NewQuicksearch and Quickmatch programs written by Peter Rice at EMBL, which are extensions of the Quicksearch programs contained in the GCG software package. You can very quickly search the EMBL database for sequences very similar to your query sequence. In addition to all entries contained in the latest EMBL release, all new EMBL and GenBank entries created since then are also accessible. -------------------------------------------------------------------------------- MAIL-FASTA Mail-FastA is based on Bill Pearson's FastA program. It allows you to perform rapid but sensitive comparisons of protein or DNA sequences against the databases. The databases available for searching include EMBL, GenBank, SwissProt and PIR. All new EMBL and GenBank entries are also accessible as soon as created. -------------------------------------------------------------------------------- Access These services are provided free of charge, though users may have to meet some of the communication costs depending o