From owner-embldatabank@net.bio.net Thu Dec 03 22:00:00 1992 Path: biosci!daresbury!news From: NETHELP@EMBL-Heidelberg.DE Newsgroups: bionet.molbio.embldatabank Subject: EMBL File Server Newsletter No. 9, Dec. 4th 1992 Message-ID: <1992Dec4.110447.15329@gserv1.dl.ac.uk> Date: 4 Dec 92 11:03:17 GMT Sender: Peter.Stoehr@DE.EMBL-Heidelberg Distribution: bionet Organization: European Molecular Biology Laboratory, Heidelberg Lines: 443 Original-To: embl-db@uk.ac.daresbury Content-Transfer-Encoding: 7BIT Original-Sender: Peter Stoehr Mime-Version: 1.0 X-Vms-To: IN%"embl-db@daresbury.ac.uk" ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 9, December 4th 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> Improvement of EMBL's Internet connectivity <3> Anonymous FTP services - alternative sites <4> New mail server command <5> Updates to data collections <6> Updates to software collection <7> Other updates <8> Summary of directories on the file server <9> Getting started ? <10> Network addresses at EMBL <1> Introduction ------------ The EMBL File Server is a facility available on the EMBL computing system for external users to request files by electronic mail, anonymous FTP or Gopher. The service is free. <2> Improvement of EMBL's Internet connectivity ------------------------------------------- Recently there has been a improvement in EMBL's Internet connection which results in considerably faster access to our anonymous FTP server and to our Gopher server, and also a quicker response to e-mail file server requests. Please note that the FTP and Gopher servers both run on FTP.EMBL-Heidelberg.DE (192.54.41.33) Do not use the host name EMBL-Heidelberg.DE <3> Anonymous FTP services - alternative sites (a) The anonymous FTP archives at EMBL are mirrored by an FTP server managed by the Israeli EMBnet national node (INN) at the Weizmann Institute. Internet address: sunbcd.weizmann.ac.il (b) Complete copies of the EMBL quarterly releases are also available by anonymous FTP from: - Swiss EMBnet Node, Biozentrum der Universitaet Basel (Switzerland) Internet address: bioftp.unibas.ch [131.152.8.1] Maintained by Reinhard Doelz (doelz@comp.bioz.unibas.ch) Plain ASCII flat files. See the file DESCRIPTION in the top level directory for more information, also on other formats of data. - Department of Molecular Biology Massachusetts General Hospital Internet address: amber.mgh.harvard.edu [132.183.190.26] Maintained by Mike Cherry (CHERRY@Frodo.MGH.Harvard.EDU) Compressed EMBL flat files. See the 000readme.txt file in the EMBL directory for more information, also on other formats of data. <4> New mail server command ----------------------- The SIZE command was added to the set of commands recognised by the EMBL e-mail server. Because some mailer systems have a maximum file size limitation the EMBL mail server splits large files into parts. The default size of these packets is 95K but can be changed with the SIZE command. E.g. SIZE 30 would change the packet size to 30K, whereas SIZE 500 would set it to 500K. Note, however, that uuencoded files are stored in individual parts of 90K each on our server, so changing the packet size to larger values will have no effect on them. <5> Updates to Data Collections ------------------------------------ New databases have been added to the file server recently: (a) Steven Henikoff's BLOCKS database Henikoff, S. and Henikoff, J. G. (1991) Automated assembly of protein blocks for database searching. Nucleic Acids Res. 19, 6565-6572. E-mail server: directory BLOCKS Anonymous ftp: /pub/databases/blocks (b) A database of CpG islands in the human genome (CPGISLE) Larsen, F., Gundersen, G., Lopez, L. and Prydz, H. (1992) CpG island as Gene Markers in the Human Genome. Genomics 13, 1095-1107. E-mail server: directory CPGISLE Anonymous ftp: /pub/databases/cpgisle (c) A database of protein kinase catalytic domains (PKCDD) provided by S.K. Hanks, A.M. Quinn and T. Hunter, Salk Institute. E-mail server: directory PKCDD Anonymous ftp: /pub/databases/pkcdd (d) Pre-release data from the Brookhaven Protein Data Bank (PDB) are now available in addition to the full releases. E-mail server: directory PROTEINDATA <6> 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: ---- AUTHORIN.UAA (N) Sequence data submission tool (Intelligenetics/DDBJ/EMBL/GenBank) [/pub/software/dos/authorin.uaa to authorin.uaf] CODONS.UUE (N) Codon usage analysis (A. Lloyd and P. Sharp) [/pub/software/dos/codons.uue] CREGEX.C (U) Conversion of PROSITE to Prosearch format v1.2 (J. Leunissen) [/pub/software/dos/cregex.c] DOTPLOT.UUE (N) Dot plot analysis (R> Nakisa) [/pub/software/dos/dotplot.uue] ESEE.UAA (U) Multiple sequence alignment editor v1.09e (E. Cabot) [/pub/software/dos/esee.uaa to esee.uac] FASTMAP.UAA (N) Approx. multipoint lod score calculation (D. Curtis) [/pub/software/dos/fastmap.uaa to fastmap.uac] GEPASI.UAA (N) Modelling of metabolic pathways (P. Mendes) [/pub/software/dos/gepasi.uaa to gepasi.uai] MACAW105.UAA (U) Multiple sequence editor v1.05 (G. Schuler) [/pub/software/dos/macaw105.uaa and macaw105.uab] PEDRAW14.UAA (U) Pedigree drawing program v1.4 (D. Curtis) [/pub/software/dos/pedraw14.uaa to pedraw14.uae] RAMHA.UAA (N) Monte Carlo simulation of random mutagenesis synthetic cDNA (D. Siderovski) [/pub/software/dos/ramha.uaa and ramha.uab] SAR2PCIT.UUE (N) Conversion of SeqAnalRef to ProCite format (E. Sonnhammer) [/pub/software/dos/sar2pcit.uue] SORFIND.UAA (N) Prediction of exons in vertebrate genomic DNA (G. Hutchinson) [/pub/software/dos/sorfind.uaa and sorfind.uab] TRBBS.UAA (N) File exchange program for automated fluorescent DNA sequencer data (I. Consani) [/pub/software/dos/trbbs.uaa and trbbs.uab] Mac: ---- AUTHORIN.HQX (N) Sequence data submission tool (Intelligenetics/DDBJ/EMBL/GenBank) [/pub/software/mac/authorin.hqx] DATAMINDER.HQX (N) Data management tools for molecular biologists (K. Usdin) [/pub/software/mac/dataminder.hqx] EMBL-SEARCH.HQX (U) Database retrieval software for EMBL CD-ROM v2.1.1 (EMBL Data Library) [/pub/software/mac/embl-search.hqx] EMBL-SEARCH_SRC.HQX (N) Source code for EMBL-Search v2.1.1 [/pub/software/mac/embl-search_src.hqx] GBSEARCH-NCBI.HQX (U) Tool to assist access to GenBank servers at NCBI v2.0.2 (D. Gilbert) [/pub/software/mac/gbsearch-ncbi.hqx] GELREADER_FPU.HQX (N) NCSA's GelReader software for Macs with FPU [/pub/software/mac/gelreader_fpu.hqx] GELREADER_NO_FPU.HQX (N) NCSA's GelReader software for Macs w/o FPU [/pub/software/mac/gelreader_no_fpu.hqx] GELREADER_SAMPLES.HQX (N) Example files for NCSA's GelReader [/pub/software/mac/gelreader_samples.hqx] HYPERPCR.HQX (N) Calculation of PCR conditions (B. Osborne) [/pub/software/mac/hyperpcr.hqx] LOOPDLOOP.HQX (N) Tool for drawing RNA structures (D. Gilbert) [/pub/software/mac/loopdloop.hqx] MACPATTERN.HQX (U) Protein pattern searching with PROSITE and BLOCKS database v.2.0.1 (R. Fuchs) [/pub/software/mac/macpattern.hqx] MACT_GENERAL.HQX (N) MacT package for phylogenetic tree calculation (general programs and documentation) (Luettke) [/pub/software/mac/mact_general.hqx] MACT_TREE26.HQX (N) MacT package for phylogenetic tree calculation (TREE26 programs for up to 26 sequences) (Luettke) [/pub/software/mac/mact_tree26.hqx] MACT_TREE4.HQX (N) MacT package for phylogenetic tree calculation (TREE4 programs for four sequences) (Luettke) [/pub/software/mac/mact_tree4.hqx] MACT_TREE5.HQX (N) MacT package for phylogenetic tree calculation (TREE5 programs for five sequences) (Luettke) [/pub/software/mac/mact_tree5.hqx] PUPKIT.HQX (N) TrueType and Postscript fonts for displaying sequences in Puppy and Kitty representation (U. Melcher) [/pub/software/mac/pupkit.hqx] PUPPY.HQX (U) Special display of nucleic acid and protein sequences v2.0 (U. Melcher) [/pub/software/mac/puppy.hqx] STUFFITLITE.HQX (U) Compression/decompression/binhex program v3.0.3 (R. Lau) [/pub/software/mac/stuffitlite.hqx or stuffitlite.sea] YEASTSTRAINS.HQX (U) Strain management, in particular yeast (K. Froehlich) [/pub/software/mac/yeaststrains.hqx] UNIX: ----- CREGEX.C (U) Conversion of PROSITE to Prosearch format v1.2 (J. Leunissen) [/pub/software/unix/cregex.c] ICATOOLS.UAA (N) Clustering and statistical analysis of large cDNA collections (J. Parsons) [/pub/software/unix/icatools.tar.Z] ICRF_CTG.UAA (N) Tools for ordering clone libraries based on hybridisation data (R. Mott and A. Grigoriev) [/pub/software/unix/icrf_ctg.tar.Z] ISSC.UAA (U) Sensitive sequence alignment package (Oct 92) (P. Argos et al.) [/pub/software/unix/issc.tar.Z] MAILFASTA.UUE (U) Script for using EMBL/GenBank Mail-FASTA servers v3.0 (T. deBoer) [/pub/software/unix/mailfasta.tar.Z] OVERSEER.UAA (U) Package for searching nucleic acid databases (Oct 92) (P. Sibbald) [/pub/software/unix/overseer.tar.Z] STATUS.UAA (N) Tools for managing large DNA-sequencing projects (M. Dubnik) [/pub/software/unix/status.tar.Z] ProtQuiz (N) Xwindows protein 3D/1D display (only available (M.Scharf, C.Sander) from FTP server) [/pub/software/unix/protquiz/ProtQuiz-0.9.tar.Z] VAX: ---- CDACCESS.UAA (U) Driver software for reading ISO CD-ROMs v2.05 (P. Stockwell) [/pub/software/vax/cdaccess.uaa and cdaccess.uab] CREGEX.C (U) Conversion of PROSITE to Prosearch format v1.2 (J. Leunissen) [/pub/software/vax/cregex.c] GENEIDSHELLS.SHARE (N) DCL shells for using GENEID server (F. Macrides) [/pub/software/vax/geneidshells.share] GRAILSHELLS.SHARE (N) DCL shells for using GRAIL server (F. Macrides) [/pub/software/vax/grailshells.share] ICATOOLS.UAA (N) Clustering and statistical analysis of large cDNA collections (J. Parsons) [/pub/software/vax/icatools.uaa to icatools.uai] ISSC.UAA (U) Sensitive sequence alignment package (Oct 92) (P. Argos et al.) [/pub/software/unix/issc.uaa to issc.uak] NCBISHELLS.SHARE (N) DCL shells for using GenBank servers (F. Macrides) [/pub/software/vax/ncbishells.share] OVERSEER.UAA (U) Package for searching nucleic acid databases (Oct 92) (P. Sibbald) [/pub/software/unix/overseer.uue] SCRUTINE.UAA (U) Scrutineer, sequence database analysis, Nov 1992 (P. Sibbald) [/pub/softare/vax/scrutine.uaa to scrutine.uai] <7> Other updates ------------- (a) A new directory that will hold information for crystallographers, XRAY. The only file currently present is the list of e-mail addresses of crystallographers and related scientists maintained by M. Teeter, Boston College. E-mail server: directory XRAY Anonymous ftp: /pub/databases/xray (b) ALIGN directory: DS11144.DAT - Alignment of insect mtDNA and ND1 gene products. Submitted by D. Pashley, 12-Jun-1992 DS12100.DAT - Alignment of small subunit rRNAs from higher fungi. Submitted by J. Suguyama, 4-Sep-1992 <8> Summary of directories on the file server --------------------------------------- directories with updated information are marked by an asterisk. Anonymous ftp NetServ -------------- --------- * EMBL Nucleotide Sequence Database /pub/databases/embl NUC (Rel. 33, Dec 92 + updates) * Eukaryotic Promotor Database /pub/databases/epd EPD (Rel. 33, Nov 92) * SwissProt Protein Sequence Database /pub/databases/swissprot PROT (Rel. 23, Aug 92 + updates) * Prosite pattern database /pub/databases/prosite PROSITE (Rel. 9.10, Aug 92) * ENZYME database /pub/databases/enzyme ENZYME (Rel. 10.00, Aug 92) * Brookhaven Protein Databank not available PROTEINDATA (Rel. 61, Jul 92 + pre-release) * REBASE, Restriction Enzyme Database /pub/databases/rebase REBASE (Rel. 9212, Dec 92) tRNA sequence and gene sequence db /pub/databases/trna TRNA (1991) * TFD, Transcription Factor Database /pub/databases/tfd TFD (Ver 5.5, Nov 92) * ECD, E.coli Database /pub/databases/ecd ECD (Rel. 13, Nov 92) * FLYBASE, Drosophila Genetic Map db /pub/databases/flybase FLYBASE (9209, 8-Sep-1992) * LiMB, Listing of Mol. Biol. db's /pub/databases/limb LIMB (Rel. 3.0) * SEQANALREF, Seq. analysis refs /pub/databases/reflist REFLIST (Rel. 32, Oct 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 (Rel. 2, Dec 1992) 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 (May 1992) 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) * CpG Islands Database /pub/databases/cpgisle CPGISLE (Pre-release 1.0, Oct 92) * Blocks database /pub/databases/blocks BLOCKS (Rel. 5.0, Jun 92) * HSSP, sequence-aligned protein /pub/databases/protein_extras/hssp families PROTEINDATA * FSSP, structure-aligned protein /pub/databases/protein_extras/fssp families (ftp only) * DSSP, protein secondary structures /pub/databases/protein_extras/dssp PROTEINDATA * pdb_select, representative sets of /pub/databases/protein_extras/ 3D proteins (ftp only) pdb_select 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 * Crystallographer's information /pub/databases/xray XRAY <9> 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. To use the Gopher server, open a connection to FTP.EMBL-Heidelberg.DE at the standard Gopher port 70. <10> 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 From owner-embldatabank@net.bio.net Fri Dec 04 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!wupost!uunet!mcsun!sunic!bio.embnet.se!embnet.se!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Alternative database update and syncing Message-ID: <1992Dec5.160851.20187@comp.bioz.unibas.ch> Date: 5 Dec 92 16:08:51 GMT Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 49 Xref: biosci bionet.molbio.genbank:1100 bionet.molbio.embldatabank:123 Nntp-Posting-Host: biox.embnet.unibas.ch In the past, there was much discussion going on with respect to the desired mechanism of feeding updates per news and polling them via ftp. Both mechanisms lack the feature of synchronisation, i.e. the only way to be sure that you have all the database entries is to ftp the whole updates. Networking in the previuos years might have worked this way. However, if hundreds of researchers do this, we run into massive bandwith problems. I have developed a different scheme witch runs on top of the HASSLE protocol (Hierarchical Access System for Sequence Libraries in Europe). The documentation is not ready yet but the client software will be available, as well as the database tools. Usage is curretly only anticipated for the EMBL database. The idea is that you send a datafile to a server containing all the entries as a listing (for simplicity, I sticked to Peter Stoehr's internal routines which list entry name, accession number, version number, and date of entry) and the server compares this list with its own database. Then, a file is created which contains all the entries the client misses, and is sent back to the client. If there's a need the entries can be decomposed into single files at the client's end. The data transmission runs asyncronously on a special socket (port 375), and uses on-the-fly compression and encryption. Accounting and security are standard. Alternative mechanisms include a request to send all new entries since a given date, and the full daily update release. The software currently runs on VAX/VMS with UCX,TCPWARE or MULTINET, and IRIX,SunOS and ULTRIX. It was developed on a Silicon Graphics running the CodeVision environment. Thanks go to Lukas Rosenthaler for contributing the compression code, and to Basel University and the Swiss National Science Foundation for grant support. Mail me if you are interested. Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-embldatabank@net.bio.net Thu Dec 10 22:00:00 1992 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!zaphod.mps.ohio-state.edu!sdd.hp.com!caen!batcomputer!cornell!uw-beaver!news.u.washington.edu!serval!cosy.chem.wsu.edu!alam From: alam@cosy.chem.wsu.edu (Steve Alam) Newsgroups: bionet.molbio.embldatabank Subject: Complete sequence for Pet3D Message-ID: <1992Dec10.190516.4827@serval.net.wsu.edu> Date: 10 Dec 92 19:05:16 GMT Sender: news@serval.net.wsu.edu (USENET News System) Organization: Washington State University Lines: 10 Keywords: We're lost Help! We are running into trouble in trying to decifer the DNA sequence of Pet3D expression vector near the areas where the multiple cloning site was placced into Pbr322. Does anybody have the complete sequence of the regions upstream of the T7 promoter and downstream of the terminator?? Or can anybody give us an idea on how to obtain it? Thanx a bunch... From the NW From owner-embldatabank@net.bio.net Thu Dec 17 22:00:00 1992 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: EMBL CD-ROM Dec. 92 is ready Message-ID: <1992Dec18.153856.60125@embl-heidelberg.de> Date: 18 Dec 92 14:38:56 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 31 The December 1992 issue of the EMBL CD-ROM (2 disks) is now being distributed, as well as release 33 of the EMBL Nucleotide Sequence Database on tape. We anticipate that all orders are shipped before Christmas. The CD-ROM contains several databases as follows: EMBL Nucleotide Sequence Database (EMBL Data Library) Swiss-Prot Protein Sequence Database (Amos Bairoch & EMBL Data Library) + Berlin RNA database (T. Specht et al) BLOCKS database (Steven Henikoff) EPD, Eukaryotic Promoter Database (Philip Bucher) ECD, E. coli database (Manfred Kroeger) CpG Island database (F. Larsen et al) CUTG, codon usage tables (K. Wada et al) ENZYME database (Amos Bairoch) HSSP, structure-sequence alignments (Reinhard Schneider, Chris Sander) KABAT dictionary of sequences of immunological interest (Elvin Kabat) PROSITE pattern database (Amos Bairoch) REBASE, Restriction enzyme database (Rich Roberts) FlyBase, Drosophila genetic map database (Michael Ashburner) HaemB, Haemophilia B database (George Brownlee) RLDB, Reference Library Database (Georg Zehetner) PKCDD, Protein Kinase Catalytic Domain database (Steven Hanks et al) rRNA, ribosomal RNA database (Rupert De Wachter et al) SeqAnalRef, sequence analysis bibliography (Amos Bairoch) TFD, Transcription Factor database (David Ghosh) tRNA, transfer RNA sequence database (M. Sprinzl et al) SmallRNA, database of small RNA sequences (S. Gupta, R. Reddy) Peter Stoehr EMBL Data Library From owner-embldatabank@net.bio.net Thu Dec 17 22:00:00 1992 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: EMBL rel. 33 release notes (extracts) Message-ID: <1992Dec18.155049.60126@embl-heidelberg.de> Date: 18 Dec 92 14:50:49 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 97 The following are some extracts from the release notes of release 33 of the EMBL Nucleotide Sequence Database, December 1992. Comments are welcome, either via the BIOSCI newsgroup bionet.molbio.embldatabank, or by e-mail to datalib@embl-heidelberg.de -------------------------- A breakdown of Release 33 by taxonomic division is shown below: Division Entries Nucleotides ----------------- ------- ----------- Bacteriophage 825 1077956 Fungi 3675 6948386 Invertebrates 9014 11077413 Organelles 2925 4272437 Other Mammals 3075 4049195 Other Vertebrates 3859 4652366 Plants 5369 6681381 Primates 22165 21151438 Prokaryotes 10926 18322905 Rodents 14189 15963099 Synthetic 1309 1096823 Unclassified 2658 2393182 Viruses 9111 13727398 ----------------- ------- ----------- Total 89100 111413979 This represents an increase of about 12% from release 32. 2 FORTHCOMING CHANGES 2.1 RA Line Author Name Format As from Release 34 in March 1993 we will change the format of author names on RA lines to conform to that used by major bibliographic databases such as Medline. The main change is that the periods which currently appear within initials will not appear any more. For example, the current: RA Wilson A., Smith B.G.; will then appear as: RA Wilson A, Smith BG; 2.2 Patent Sequences A collaboration between the EMBL Data Library and the European Patent Office will enable us to include patent sequences in our quarterly distributions as from Release 34 in March 1993. These sequences will each have a new patent reference type, to document the source of the data. Patent-specific information will appear in the RL line block (introduced by the keyword "Patent") and the other reference linetypes (RN, RP, RC, RA, RT) will appear as usual. An example of a patent RL line block is shown below: RL Patent number EP0062971-A/1, 20-OCT-1982. RL IMPERIAL CHEMICAL INDUSTRIES PLC. RL UNIVERSITY OF LEICESTER. The date on the first line in the RL block is the publication date of the patent, and the following line(s) list the patent applicant(s). 2.3 Molecule Topology As from Release 35 in June 1993 we will indicate molecules which are known to be circular by prefixing the molecule type on the ID line with the keyword "circular". Other topology keywords may appear in the same location at future releases. Please note that the absence of the keyword "circular" should *not* be taken to indicate that the molecule is definitely known not to be circular. An example of such a circular molecule's ID line is shown below: ID CLSPC1 standard; circular DNA; ROD; 346 BP. 2.4 Sequence Numbering To aid reading the sequence bases in database entries, we will insert base numbers in columns 73-80 of each sequence line as from Release 35 in June 1993. The numbers will be right justified, and will indicate the number of the last base on each line. An example is shown below (the ruler is for your convenience and will not appear in the database entries): 1 10 20 30 40 50 60 70 80 +--------+---------+---------+---------+---------+---------+---------+---------+ SQ Sequence 245 BP; 60 A; 44 C; 77 G; 64 T; 0 other; agatcttctg ctcccaggag agagagcaat gtctagagta gggaaaagga ccatcttagc 60 cctctactat aggcagctgt ctgctacccg tcactcacca atgggagagg aggcatgggt 120 attgtgttca gatggggccc agtgttattt atttgagact ggatcagggt gagaacttga 180 ggggaagggt tggagtagaa ggttatgatc tttctagaca gtgctgcatt ggtggcttga 240 ctgac 245 // +--------+---------+---------+---------+---------+---------+---------+---------+ 1 10 20 30 40 50 60 70 80 From owner-embldatabank@net.bio.net Thu Dec 17 22:00:00 1992 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!magnus.acs.ohio-state.edu!usenet.ins.cwru.edu!agate!doc.ic.ac.uk!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: Re: EMBL CD-ROM Dec. 92 is ready Message-ID: <1992Dec18.170620.60127@embl-heidelberg.de> Date: 18 Dec 92 16:06:20 GMT References: <1992Dec18.153856.60125@embl-heidelberg.de> Organization: EMBL, European Molecular Biology Laboratory Lines: 9 In article <1992Dec18.153856.60125@embl-heidelberg.de>, stoehr@embl-heidelberg.de writes: > RLDB, Reference Library Database (Georg Zehetner) Sorry, that should be Guenther Zehetner. Peter Stoehr EMBL Data Library From owner-embldatabank@net.bio.net Tue Dec 22 22:00:00 1992 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Re: EMBL <> GenBank Message-ID: <1992Dec23.081643.11004@comp.bioz.unibas.ch> Date: 23 Dec 92 08:16:43 GMT References: <1992Dec22.142144.18782@husc3.harvard.edu> <1992Dec22.220954.563@nlm.nih.gov> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 76 Xref: biosci bionet.molbio.genbank:1133 bionet.molbio.embldatabank:128 Nntp-Posting-Host: biox.embnet.unibas.ch In article <1992Dec22.220954.563@nlm.nih.gov>, ostell@object.nlm.nih.gov (Jim Ostell) writes: |> Actually there are a large number of differences between EMBL and |> GenBank, including entries with the same primary accession but |> different sequences in EMBL and GenBank, entries with the same |> sequence but different primary accessions in EMBL and GenBank, |> and all sorts of other varients. There are a variety of reasons ... It has been brought to our attention by one of our customers that there are currently thousands (!) of these cases. In contrast to the original assumption that Genbank 74 will now be sort of identical to EMBL 33, I can only warn all of you who trusted in this rather than trying it out. Actually, if you take one of the applications doing accession number exclusion (I use the GCG package for this purpose here), I get more than 10000 entries which show accession numbers that are not in EMBL 33 but in GENBANK 74 ... the listing keyed by division is shown here: Gb_Ba: Entries: 1,715 Accession Numbers: 2,692 Gb_In: Entries: 1,037 Accession Numbers: 1,494 Gb_Om: Entries: 446 Accession Numbers: 634 Gb_EST: Entries: 1,000 Accession Numbers: 1,000 Gb_Ov: Entries: 487 Accession Numbers: 694 Gb_Ph: Entries: 76 Accession Numbers: 134 Gb_Pl: Entries: 1,707 Accession Numbers: 2,512 Gb_Pr: Entries: 3,096 Accession Numbers: 3,743 Gb_Ro: Entries: 1,933 Accession Numbers: 2,601 Gb_St: Entries: 61 Accession Numbers: 63 Gb_Sy: Entries: 5 Accession Numbers: 5 Gb_Un: Entries: 8 Accession Numbers: 8 Gb_Vi: Entries: 747 Accession Numbers: 938 The statistics read as follows: Numbers total Primary numbers D... 1093 1027 J... 15 3 K... 4 2 L... 219 219 M... 966 107 S... 2900 2899 V... 3 0 X... 468 6 Z... 30 6 Total 5698 4269 The only thing which is not clear to me is, then, why these 5700 numbers are present in more than 15000 Genbank entries. Clearly a point where a cleanup might be necessary... Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ ----------------------------------------- From owner-embldatabank@net.bio.net Tue Dec 22 22:00:00 1992 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!stoehr From: stoehr@embl-heidelberg.de Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Re: EMBL <> GenBank Message-ID: <1992Dec23.160654.60156@embl-heidelberg.de> Date: 23 Dec 92 15:06:54 GMT References: <1992Dec22.142144.18782@husc3.harvard.edu> <1992Dec22.220954.563@nlm.nih.gov> <1992Dec23.081643.11004@comp.bioz.unibas.ch> Organization: EMBL, European Molecular Biology Laboratory Lines: 23 Xref: biosci bionet.molbio.genbank:1134 bionet.molbio.embldatabank:129 In article <1992Dec23.081643.11004@comp.bioz.unibas.ch>, doelz@comp.bioz.unibas.ch (Reinhard Doelz) writes: > > It has been brought to our attention by one of our customers that there > are currently thousands (!) of these cases. In contrast to the original > assumption that Genbank 74 will now be sort of identical to EMBL 33, I > can only warn all of you who trusted in this rather than trying it out. > Firstly, the assumption that GenBank 74 should be 'sort of identical' to EMBL 33 is false (depending on how identical 'sort of' means). The two databases are made at different times. We do not yet have Genbank 74 here: when we do, as for other quarterly releases, we determine what we are missing and work to include it all in the EMBL database. I'm surprised at the figure of 10,000, as I believe that when we made EMBL 33 that all acc#'s from the previous GenBank release were in. Another current difference is the accession numbers beginning with 'S' (about 3000 according to your figures) which we do not include in EMBL yet - but that's a different story. Regards, Peter Stoehr EMBL Data Library From owner-embldatabank@net.bio.net Tue Dec 22 22:00:00 1992 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!rdoelz From: rdoelz@comp.bioz.unibas.ch [remote] (Reinhard Doelz) Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: Re: EMBL <> GenBank Message-ID: <1992Dec23.193147.21458@comp.bioz.unibas.ch> Date: 23 Dec 92 19:31:47 GMT References: <1992Dec22.142144.18782@husc3.harvard.edu> <1992Dec22.220954.563@nlm.nih.gov> <1992Dec23.081643.11004@comp.bioz.unibas.ch> <1992Dec23.160654.60156@embl-heidelberg.de> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Organization: EMBnet Switzerland [BASEL] Lines: 63 Xref: biosci bionet.molbio.genbank:1135 bionet.molbio.embldatabank:130 Nntp-Posting-Host: biox.embnet.unibas.ch In article <1992Dec23.160654.60156@embl-heidelberg.de>, stoehr@embl-heidelberg.de writes: |> In article <1992Dec23.081643.11004@comp.bioz.unibas.ch>, |> doelz@comp.bioz.unibas.ch (Reinhard Doelz) writes: |> > |> > It has been brought to our attention by one of our customers that there |> > are currently thousands (!) of these cases. In contrast to the original |> > assumption that Genbank 74 will now be sort of identical to EMBL 33, I |> > can only warn all of you who trusted in this rather than trying it out. |> > |> |> Firstly, the assumption that GenBank 74 should be 'sort of identical' to |> EMBL 33 is false (depending on how identical 'sort of' means). The two |> databases are made at different times. Sorry if this sounds misleading - I trusted in the release notes stating "New and updated sequence data from the latest GenBank and DDBJ releases have been incorporated into this release." Freeze date EMBL Release 33 on 8 November 1992, GENBANK 74 on 17 November 1992 - I thought that this would imply the most recent daily updates from GENBANK also to be in EMBL and vice versa. |> We do not yet have Genbank 74 here: when we do, as for other quarterly |> releases, we determine what we are missing and work to include it all in the |> EMBL database. I'm surprised at the figure of 10,000, as I believe that when |> we made EMBL 33 that all acc#'s from the previous GenBank release were in. |> Another current difference is the accession numbers beginning with 'S' (about |> 3000 according to your figures) which we do not include in EMBL yet - but |> that's a different story. I used the -exclude flag in the GCG software to compute the numbers that I quoted. The entry number is surprising to me also, and I just hope that there is an error in my procedures. With respect to the numbers; I have taken the daily EMBL updates (as of Dec 20 at EMBL creation), and the GENBANK 74 release files (not their daily updates), and came up with 8141 entries of EMBL, resembling 8540 accession numbers. (This is for both new entries from EMBL and GENBANK as sent by EMBL in EMBL format. If I look at how many entries are in GENBANK 74 not in EMBL 33 (containing 5698 AN), and subtract those which are unique to EMBL, it appears that EMBL updates contain 2591 entries which are in GENBANK 74 (according to 2612 Accession Numbers). That still leaves us with a considerable number of discrepancies. |> |> Regards, |> Peter Stoehr |> EMBL Data Library Your work is most appreciated, and I encourage you to keep up the good work. I didn't want to make any negative statements on quality in general, just point out that the exclusion sets are still a need. Regards Reinhard -- +----------------------------------+-------------------------------------+ | Dr. Reinhard Doelz | RFC doelz@urz.unibas.ch | | Biocomputing | DECNET 20579::48130::doelz | |Biozentrum der Universitaet | X25 022846211142036::doelz | | Klingelbergstrasse 70 | FAX x41 61 261- 6760 or 267- 2078 | CH 4056 Basel | TEL x41 61 267- 2076 or 2247 | +------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+ -----------------------------------------