From owner-embldatabank@net.bio.net Thu Jul 01 23:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!comp.bioz.unibas.ch!doelz From: doelz@comp.bioz.unibas.ch (Reinhard Doelz) Newsgroups: bionet.molbio.embldatabank Subject: Re: secondary accession numbers Message-ID: <1993Jul2.055206.7673@comp.bioz.unibas.ch> Date: 2 Jul 93 05:52:06 GMT References: <1993Jul1.234108.1@molbiol.ox.ac.uk> Sender: usenet@comp.bioz.unibas.ch (NEWS transaction account) Reply-To: doelz@urz.unibas.ch Followup-To: bionet.software.gcg Organization: EMBnet Switzerland [BASEL] Lines: 65 Nntp-Posting-Host: biox.embnet.unibas.ch In article <1993Jul1.234108.1@molbiol.ox.ac.uk>, rhubner@molbiol.ox.ac.uk writes: ... |> may represent *secondary* accession numbers and can not be searched for by |> FETCH (and especially STRINGSEARCH; only ref fields) in GCG. This was the ^^^ DE The problem which is described by you applies only to those secondary accession numbers which occur more than once. The accession numbers are used as identifiers in GCG. Look at the .numbers file and see biox > more /bioy/data/xembl/xembl.numbers D00410 10824 S D00515 9593 S D00683 3219 S D00684 3219 S D00739 11834 S D00819 10077 P D00821 11584 S D00844 3136 P D00849 3049 S D01022 6221 P ... 'S' for secondary and 'P' for primary. If the secondary accession number occurs only *once* then GCG will work due the fact that it is unique. In your case, /bioy/data/gcgembl/em_pr.ref:AC M18693; J03516; M18691; /bioy/data/gcgembl/em_pr.ref:AC M18694; J03516; M18691; /bioy/data/gcgembl/em_pr.ref:AC M18695; J03516; M18691; /bioy/data/gcgembl/em_pr.ref:AC M18696; J03516; M18691; /bioy/data/gcgembl/em_pr.ref:AC M18697; J03516; M18691; /bioy/data/gcgembl/em_pr.ref:AC M18698; J03516; M18691; /bioy/data/gcgembl/em_pr.ref:AC M18699; J03516; M18691; /bioy/data/gcgembl/em_pr.ref:AC M18700; J03516; M18691; /bioy/data/gcgembl/em_pr.ref:AC M18692; J03516; we can see that J03516 occurs more than once. Followups redirected to bionet.software.gcg. > The SRS software can do the job properly... I work with SRS, and can recommend the software for these purposes. Thure Etzold made the code available without cost and I appreciate this very much. The indices for the full set of sequence databases (PIR, SWISSPROT, EMBL, GENBANK exclusion) occupy only about 130 MByte disk space which is relatively little as compared to 500 MByte of data. 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 Jul 06 23:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!fuchs From: fuchs@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: EMBL File Server Newsletter 10 Message-ID: <1993Jul7.150539.100470@embl-heidelberg.de> Date: 7 Jul 93 14:05:39 GMT Reply-To: NetHelp@EMBL-Heidelberg.DE Organization: EMBL, European Molecular Biology Laboratory Lines: 480 ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 10, July 7th 1993 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 69012 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Blitz e-mail server <3> Updates to data collections <4> Updates to software collection <5> Other updates <6> Summary of directories on the file server <7> Getting started ? <8> 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> Blitz e-mail server ------------------- BLITZ is an automatic electronic mail server for the MPsrch program of Shane Sturrock and John Collins, Biocomputing Research Unit, University of Edinburgh, Scotland. MPsrch allows you to perform sensitive and extremely fast comparisons of your protein sequences against the Swiss-Prot protein sequence database using the Smith and Waterman best local similarity algorithm. It runs on the MasPar family of massively parallel machines; the BLITZ server uses a 4096-processor MasPar MP-1 system. A typical search time for a query sequence of 400 amino acids is approximately 40 seconds to search the entire Swiss-Prot database. Additional time is required to reconstruct the alignments; the time for this will depend on the number of alignments requested. MPsrch is the fastest implementation of the SW algorithm currently available on any machine. How to use BLITZ ---------------- Send a properly formatted electronic mail message to BLITZ@EMBL-Heidelberg.DE containing required commands and parameters and the answer will be automatically mailed to you. To obtain full documentation of the service and algorithms used, send a message containing just the word HELP. If you have any problems using the BLITZ service, or any questions, please send them to: NETHELP@EMBL-Heidelberg.DE Example ------- SEQ STKKKPLTQE QLEDARRLKA IYEKKKNELG LSQESVADKM GMGQSGVGAL FNGINALNAY NAALLAKILK VSVEEFSPSI AREIYEMYEA VSMQPSLRSE YEYPVFSHVQ AGMFSPELRT FTKGDAERWV STTKKASDSA FWLEVEGNSM TAPTGSKPSF PDGMLILVDP EQAVEPGDFC IARLGGDEFT FKKLIRDSGQ VFLQPLNPQY PMIPCNESCS VVGKVIASQW PEETFG END The possible parameters (eg gap penalty, weight matrix) are explained in the HELP documentation. <3> Updates to Data Collections ------------------------------------ New databases have been added to the file server since Newsletter issue 9: (a) RELIBRARY - Restriction Enzyme List, by E. Raschke Raschke, E. (1993) Comprehensive restriction enzyme lists to update any DNA sequence computer program. Genetic Analysis, Techniques and Applications, Vol. 10, in press. (b) REPBASE - Protoypic sequences for human repetitive DNA, by J. Jurka Jurka, J., Walichiewicz, J. and Milosavljevic, A. (1992) J. Mol. Evol. 35:286 (c) HLA - Alignments of human class I and II HLA sequences, by S. Marsh, J. Zemmour and P. Parham. (d) TRANSTERM - Translational termination signal database, by C. Brown Brown, C.M., Dalphin, M.E., Stockwell, P.A., Tate, W.P. (1993) Nucleic Acids Res. Supplement, submitted (e) LISTA - Compilation of nucleotide sequences encoding proteins from the yeast saccharomyces, by P. Linder Mosse, M.O., Linder, P., Lazowska, J. and Slonimski, P.P. (1993) Curr. Genet. 23, 66. <4> 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: ---- BED.UAA (N) Sequence editor with speaker feeback (R. Hwan-Seok) [/pub/software/dos/bed.uaa and .uab] BOXSHADE.UUE (N) Plots of multiple alignments with boxes and shades (K. Hofmann) [/pub/software/dos/boxshade.uue] CM.UAA (U) Restriction map construction from multiple digestion data v1.0a (K. Hofmann) [/pub/software/dos/cm.uaa to cm.uai] CONSENSE.UUE (N) Calculation of consensus sequence from alignment (S. Rensing) [/pub/software/dos/consense.uue] DIGEST.UAA (N) Restriction enzyme mapping (R. Nakisa) [/pub/software/dos/digest.uaa and digest.uab] DOTPLOT.UAA (U) Dot plot analysis v3.0 (R. Nakisa) [/pub/software/dos/dotplot.uaa and dotplot.uaa] EXPLORE.UAA (N) Analysis of multiple alignments (G. Golding) [/pub/software/dos/explore.uaa and explore.uab] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/dos/hth.c] RASMOL.UAA (N) Visualisation of macromolecules using PDB files (R. Sayle) [/pub/software/dos/rasmol.uaa to rasmol.uac] SILMUT.UUE (N) Identification of regions suitable for silent mutagenesis (B. Shankarappa) [/pub/software/dos/silmut.uue] SORFIND.UUE (U) Prediction of exons in vertebrate genomic DNA v1.7 (G. Hutchinson) [/pub/software/dos/sorfind.uue] WINBLAST.UAA (N) Windows 3.1 interface for NCBI BLAST server (A. Sivaprasad) [/pub/software/dos/winblast.uaa to winblast.uae] WINDOT.UAA (N) Dot plot analyis under Windows 3.1 (R. Nakisa) [/pub/software/dos/windot.uaa and windot.uab] WINIRX.UAA (N) Windows 3.1 interface for NCBI IRX server [/pub/software/dos/winirx.uaa to winirx.uae] WINSEQ.UUE (N) Windows version of D. Gilbert's READSEQ (R. Nakisa) [/pub/software/dos/winseq.uue] Mac: ---- ALIGN.HQX (U) Sequence alignments and phylogeny (replacement of corrupt archive) (D. Feng) [/pub/software/mac/align.hqx] AMPLIFY.HQX (U) PCR primer checks v1.2 (B. Engels) [/pub/software/mac/amplify.hqx] BKGCUCLC_FONTS.HQX (N) Color fonts for use with sequence editors (M. Sogin) [/pub/software/mac/bkgcuclc_fonts.hqx] DBCONV.HQX (U) Transformation of line-oriented databases into tab- delimited format v2.0 (J. Valverde) [/pub/software/mac/dbconb.hqx] DIGISPEAK.HQX (N) Sequence reading with sonic digitizer (N. Mantei) [/pub/software/mac/digispeak.hqx] DNAID.HQX (U) DNA sequence editor with grep-like search routine v1.8 (F. Dardel) [/pub/software/mac/dnaid.hqx] EMBL-SEARCH.HQX (U) Database retrieval software for EMBL CD-ROM v2.3.2 (EMBL Data Library) [/pub/software/mac/embl-search.hqx] EMBL-SEARCH_SRC.HQX (U) Source code for EMBL-Search v2.3.2 [/pub/software/mac/embl-search_src.hqx] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/mac/hth.c] LABHELPER.HQX (N) General laboratory tools for buffer preps etc. (T. Tzeng) [/pub/software/mac/labhelper.hqx] MACCLADE30_DEMO.HQX (N) Demo of phylogenetic analysis program (W. Maddison) [/pub/software/mac/macclade30_demo.hqx] MACP12.HQX (N) Protein property profile plots (A. Luettke) [/pub/software/mac/macp12.hqx] MACPATTERN.HQX (U) Protein pattern searching with PROSITE and BLOCKS database v3.0 (R. Fuchs) [/pub/software/mac/macpattern.hqx] MACSTAN.HQX (N) Random nucleotide sequence generator and analyzer (F. Gast) [/pub/software/mac/macstan.hqx] PROTEINSTRUCTURE.HQX (N) Tutorial on protein structures (C. Burchill) [/pub/software/mac/proteinstructure.hqx] READSEQ.HQX (U) Sequence format conversion program (D. Gilbert) [/pub/software/mac/readseq.hqx] RRNA-STACK.HQX (U) Phylogeny of 16/18S rRNA (J. Brown) [/pub/software/mac/rrna-stack.hqx] STUFFITLITE.HQX (U) Compression/decompression/binhex program v3.0.5 (R. Lau) [/pub/software/mac/stuffitlite.hqx or stuffitlite.sea] TOPPPRED.HQX (N) Prediction of transmembrane segments and their topology (G. v. Heijne, M.G. Claros) YEASTSTRAINS.HQX (U) Strain management, in particular yeast v1.2 (K. Froehlich) [/pub/software/mac/yeaststrains.hqx] UNIX: ----- BLKSRCH.UUE (N) Block search analysis of protein sequences with the BLOCKS database (R. Fuchs) [/pub/software/unix/blocksearch.tar.Z] BTAB.UAA (N) BLAST output parser (M. Dubnick) [/pub/software/unix/btab.tar.Z] double-digester.tar.Z (N) Graphical analysis of double digest restriction (only on FTP server) data (L. Wright). DTASK11S.UAA (N) Smith-Waterman database searches on parallel work- stations (G. Hauge) [/pub/software/unix/dtask11s.tar.Z] FILTER.UAA (U) Suboptimal alignments and motif recognition (P. Argos) [/pub/software/unix/filter.tar.Z] GENAL.UUE (N) Alignments of genomic sequences with coding regions (J. Stoevlbaek) [/pub/software/unix/genal.tar.Z] GM.UAA (U) Analysis of unknown DNA sequences v2.0 (C. Fields) [/pub/software/unix/gm.tar.Z] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/unix/hth.c] MAILFASTA.UUE (U) Script for using EMBL/GenBank Mail-FASTA servers v3.1 (T. deBoer) [/pub/software/unix/mailfasta.tar.Z] MOLBIO.UAA (N) C++ clas library for molecular biology (K. Robison) [/pub/software/unix/molbio.tar.Z] RASMOL.UAA (N) Visualisation of macromolecules using PDB files (R. Sayle) [/pub/software/unix/rasmol.tar.Z] READSEQ.UAA (U) Sequence format conversion program (D. Gilbert) [/pub/software/unix/readseq.tar.Z] SUPER.UAA (N) Tool for electronic user polls (R. Doelz) [/pub/software/unix/super.tar.Z] VAX: ---- BLKSRCH.UUE (N) Block search analysis of protein sequences with the BLOCKS database (R. Fuchs) [/pub/software/vax/blksrch.uue] FILTER.UAA (U) Suboptimal alignments and motif recognition (P. Argos) [/pub/software/vax/filter.uaa to filter.uad] GCGMENU.UAA (N) Menu interface to GCG package (C. Gartmann) [/pub/software/vax/gcgmenu.uaa and gcgmenu.uab] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/vax/hth.c] PDBTOGCG.FOR (N) Extracts protein sequences from PDB files (M. Mezei) [/pub/software/vax/pdbtogcg.for] READSEQ.UAA (U) Sequence format conversion program (D. Gilbert) [/pub/software/vax/readseq.uaa to readseq.uac] SUPER.UUE (N) Tool for electronic user polls (R. Doelz) [/pub/software/unix/super.uue] TFD2GCG.FOR (N) Converts TFD SITES table to GCG Prosite format (D. Mathog) [/pub/software/vax/tfd2gcg.for] UNZIP.UUE (N) Decompresses ZIP encoded files (H. Smith) [/pub/software/vax/unzip.uue] <5> 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: o DS13648.DAT - Alignment of plasmodial small subunit rRNAs. Submitted by V.Enea, 26-Feb-1993 o DS13893.DAT - Alignment of amino acid sequences derived from conceptual reading frames of Tc1-like elements from fish, nematodes, fruit flies an agnathan, and a spider. Submitted by D.H.A. Fitch, 18-Mar-1993 o DS13894.DAT - Alignment of Tc1-like elements from salmon, trout, zebrafish, and catfish. Submitted by D.H.A. Fitch, 18-Mar-1993 o DS14642.DAT - Alignment of amino acid sequences of the zinc-containing long-chain alcohol dehydrogenases. Submitted by S. Yokoyama, 17-Jun-1993 <6> 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. 35, Jun 93 + updates) * Eukaryotic Promotor Database /pub/databases/epd EPD (Rel. 35, May 93) * SwissProt Protein Sequence Database /pub/databases/swissprot PROT (Rel. 25, Apr 92 + updates) * Prosite pattern database /pub/databases/prosite PROSITE (Rel. 10.1, Apr 93) * ENZYME database /pub/databases/enzyme ENZYME (Rel. 12.00, Aug 93) * Brookhaven Protein Databank not available PROTEINDATA (Rel. 61, Jul 92 + pre-release) * REBASE, Restriction Enzyme Database /pub/databases/rebase REBASE (Rel. 9307, Jul 93) * RELIBRARY, Restriction Enzyme List /pub/databases/relibrary RELIBRARY (Apr 1993) * tRNA sequence and gene sequence db /pub/databases/trna TRNA (1993) * REPBASE - Prototypic sequences for /pub/databases/repbase REPBASE human repetitive DNA (Rel. 1.01 1992) * TFD, Transcription Factor Database /pub/databases/tfd TFD (Ver 5.5, Nov 92) * ECD, E.coli Database /pub/databases/ecd ECD (Rel. 14, Feb 93) 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. 38, Apr 93) 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, Oct 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 (Jun 1993) CUTG, codon usage /pub/databases/cutg CUTG tabulated from GenBank rel. 69 * 3D_Ali, 3D alignment database /pub/databases/3d_ali 3D_ALI (Jun 1993) * RLDB, Reference Library Database /pub/databases/rldb (Jun 1993) (ftp only) * PKCDD, Protein Kinase Catalytic /pub/databases/pkcdd PKCDD Domain Database (April 1993) * CpG Islands Database /pub/databases/cpgisle CPGISLE (Release 2.0, Apr 1992) * Blocks database /pub/databases/blocks BLOCKS (Rel. 6.0, Jan 1993) * HLA, Alignments of human HLA /pub/databases/hla HLA sequences (Jul 1993) * TRANSTERM, Translational /pub/databases/transterm TRANSTERM Termination Signal Database (Apr 1993) * LISTA, Yeast coding sequences /pub/databases/lista LISTA (Rel. 2.0, Apr 1993) * 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 (Sep 1992) (ftp only) pdb_select Misfolded, database of deliberately /pub/database/protein_extras/misfolded misfolded protein models (Nov 92) (ftp only) 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 * Crystallographers' information /pub/databases/xray XRAY <7> 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. <8> Network addresses at EMBL ------------------------- EMBL File Server (e-mail requests) NetServ@EMBL-Heidelberg.DE Anonymous FTP FTP.EMBL-Heidelberg.DE BLITZ e-mail server Blitz@EMBL-Heidelberg.DE FASTA e-mail server FASTA@EMBL-Heidelberg.DE Quicksearch e-mail server Quick@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 Tue Jul 06 23:00:00 1993 Path: biosci!agate!spool.mu.edu!uunet!newsflash.concordia.ca!mizar.cc.umanitoba.ca!frist From: frist@ccu.umanitoba.ca Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank Subject: "source" feature key Keywords: GenBank EMBL DDBJ feature table Message-ID: Date: 7 Jul 93 17:52:22 GMT Sender: news@ccu.umanitoba.ca Followup-To: bionet.molbio.genbank Organization: University of Manitoba, Winnipeg, Manitoba, Canada Lines: 84 Xref: biosci bionet.molbio.genbank:1335 bionet.molbio.embldatabank:206 Nntp-Posting-Host: norton.cc.umanitoba.ca The current Feature Table Definition (Version 1.04) describes a new feature key: - - - - - - - - - - - - - - (from FT Definition) - - - - - - - - - - - - Feature key source Definition: identifies the biological source of the specified span of the sequence. This key is mandatory. Every entry will have, as a minimum, a single source key spanning the entire sequence. More than one source key per sequence is permittable. Mandatory qualifiers: /organism="text" Optional qualifiers: a whole bunch, including /label=feature_label - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This is a very welcome addition to the Feature Table (FT) language. However, I have some questions. 1) Source is does not appear to be implemented as of GenBank Release 77.0. Is it likely to be implemented soon? Has it only been implemented in new entries, so that I just haven't seen it yet? 2) Can we have a few working examples of source in use? There are a number of usage conventions that need to be agreed upon. Let me propose that it might be very convenient if the 'source' label field was just the ORIGINAL accession number for that span: ORIGINAL entry: source 1..1089 /label=X12345 /organism="Unicornus mythicalis" exon 103..712 /label=X12345:exon1 /note="This feature added for illustrative purposes" SAME FEATURES AFTER MERGER INTO LARGER ENTRY: source 134231..135319 /label=X12345 /organism="Unicornus mythicalis" exon 134333..134942 /label=X12345:exon1 /note="This feature added for illustrative purposes" Note that I am proposing the convention that all features other than source have labels that are FT expressions, incorporating the original accession number. This convention ensures that each label is UNIQUE ACROSS THE ENTIRE DATABASE, and NEVER CHANGES. To illustrate a point, one might merge a bunch of sequences representing a chromosomal region into a larger entry. Prior to merger, many of the component entries might have features labled "exon1", and so their labels would be ambigous. Incorporating the accession # into the label prevents this probelem. Another ramification of the conventions I have shown is that even base ranges remain valid. For example: X12345:103..712 would still return the same exon from the original entry prior to merger, because the software can reconstruct X12345 from the new entry. It is my feeling that we need to build mechanisms like this into the databases that will protect FT expressions from obsolescence. Using conventions such as this, one can maintain lists of expressions that will always retrieve the same sequence, regardless of how much merging and correction goes on among entries. 3) The wording of the definition implies that every entry must now have a Feature Table, even if only to have a source field. Is that true? I guess I've done more than simply ask questions here, but I think these points were worth bringing up. =============================================================================== Brian Fristensky | Department of Plant Science | A question is like a knife that slices University of Manitoba | through the stage backdrop and gives us Winnipeg, MB R3T 2N2 CANADA | a look at what lies hidden behind. frist@ccu.umanitoba.ca | Office phone: 204-474-6085 | Milan Kundera, THE UNBEARABLE LIGHTNESS FAX: 204-261-5732 | OF BEING =============================================================================== From owner-embldatabank@net.bio.net Tue Jul 06 23:00:00 1993 Path: biosci!EMBL-Heidelberg.DE From: Rainer.Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs (EMBL Data Library)) Newsgroups: bionet.announce,bionet.molbio.embldatabank Subject: EMBL Newsletter 10 Message-ID: <1993Jul7.145406.100469@embl-heidelberg.de> Date: 7 Jul 93 13:55:04 GMT Sender: kristoff@net.bio.net Reply-To: NetHelp@EMBL-Heidelberg.DE Followup-To: bionet.molbio.embldatabank Organization: EMBL, European Molecular Biology Laboratory Lines: 481 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.announce:610 bionet.molbio.embldatabank:205 ------------------------------------------------------------------------------ | EMBL FILE SERVER News Number 10, July 7th 1993 | | | | European Molecular Biology Laboratory, Data Library & Computer Group, | | Postfach 10.2209, 69012 Heidelberg, Germany. | | Tel: +49 6221 387258 | | E-mail: NetHelp@EMBL-Heidelberg.DE Fax: +49 6221 387519 | ------------------------------------------------------------------------------ Contents: <1> Introduction <2> Blitz e-mail server <3> Updates to data collections <4> Updates to software collection <5> Other updates <6> Summary of directories on the file server <7> Getting started ? <8> 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> Blitz e-mail server ------------------- BLITZ is an automatic electronic mail server for the MPsrch program of Shane Sturrock and John Collins, Biocomputing Research Unit, University of Edinburgh, Scotland. MPsrch allows you to perform sensitive and extremely fast comparisons of your protein sequences against the Swiss-Prot protein sequence database using the Smith and Waterman best local similarity algorithm. It runs on the MasPar family of massively parallel machines; the BLITZ server uses a 4096-processor MasPar MP-1 system. A typical search time for a query sequence of 400 amino acids is approximately 40 seconds to search the entire Swiss-Prot database. Additional time is required to reconstruct the alignments; the time for this will depend on the number of alignments requested. MPsrch is the fastest implementation of the SW algorithm currently available on any machine. How to use BLITZ ---------------- Send a properly formatted electronic mail message to BLITZ@EMBL-Heidelberg.DE containing required commands and parameters and the answer will be automatically mailed to you. To obtain full documentation of the service and algorithms used, send a message containing just the word HELP. If you have any problems using the BLITZ service, or any questions, please send them to: NETHELP@EMBL-Heidelberg.DE Example ------- SEQ STKKKPLTQE QLEDARRLKA IYEKKKNELG LSQESVADKM GMGQSGVGAL FNGINALNAY NAALLAKILK VSVEEFSPSI AREIYEMYEA VSMQPSLRSE YEYPVFSHVQ AGMFSPELRT FTKGDAERWV STTKKASDSA FWLEVEGNSM TAPTGSKPSF PDGMLILVDP EQAVEPGDFC IARLGGDEFT FKKLIRDSGQ VFLQPLNPQY PMIPCNESCS VVGKVIASQW PEETFG END The possible parameters (eg gap penalty, weight matrix) are explained in the HELP documentation. <3> Updates to Data Collections ------------------------------------ New databases have been added to the file server since Newsletter issue 9: (a) RELIBRARY - Restriction Enzyme List, by E. Raschke Raschke, E. (1993) Comprehensive restriction enzyme lists to update any DNA sequence computer program. Genetic Analysis, Techniques and Applications, Vol. 10, in press. (b) REPBASE - Protoypic sequences for human repetitive DNA, by J. Jurka Jurka, J., Walichiewicz, J. and Milosavljevic, A. (1992) J. Mol. Evol. 35:286 (c) HLA - Alignments of human class I and II HLA sequences, by S. Marsh, J. Zemmour and P. Parham. (d) TRANSTERM - Translational termination signal database, by C. Brown Brown, C.M., Dalphin, M.E., Stockwell, P.A., Tate, W.P. (1993) Nucleic Acids Res. Supplement, submitted (e) LISTA - Compilation of nucleotide sequences encoding proteins from the yeast saccharomyces, by P. Linder Mosse, M.O., Linder, P., Lazowska, J. and Slonimski, P.P. (1993) Curr. Genet. 23, 66. <4> 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: ---- BED.UAA (N) Sequence editor with speaker feeback (R. Hwan-Seok) [/pub/software/dos/bed.uaa and .uab] BOXSHADE.UUE (N) Plots of multiple alignments with boxes and shades (K. Hofmann) [/pub/software/dos/boxshade.uue] CM.UAA (U) Restriction map construction from multiple digestion data v1.0a (K. Hofmann) [/pub/software/dos/cm.uaa to cm.uai] CONSENSE.UUE (N) Calculation of consensus sequence from alignment (S. Rensing) [/pub/software/dos/consense.uue] DIGEST.UAA (N) Restriction enzyme mapping (R. Nakisa) [/pub/software/dos/digest.uaa and digest.uab] DOTPLOT.UAA (U) Dot plot analysis v3.0 (R. Nakisa) [/pub/software/dos/dotplot.uaa and dotplot.uaa] EXPLORE.UAA (N) Analysis of multiple alignments (G. Golding) [/pub/software/dos/explore.uaa and explore.uab] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/dos/hth.c] RASMOL.UAA (N) Visualisation of macromolecules using PDB files (R. Sayle) [/pub/software/dos/rasmol.uaa to rasmol.uac] SILMUT.UUE (N) Identification of regions suitable for silent mutagenesis (B. Shankarappa) [/pub/software/dos/silmut.uue] SORFIND.UUE (U) Prediction of exons in vertebrate genomic DNA v1.7 (G. Hutchinson) [/pub/software/dos/sorfind.uue] WINBLAST.UAA (N) Windows 3.1 interface for NCBI BLAST server (A. Sivaprasad) [/pub/software/dos/winblast.uaa to winblast.uae] WINDOT.UAA (N) Dot plot analyis under Windows 3.1 (R. Nakisa) [/pub/software/dos/windot.uaa and windot.uab] WINIRX.UAA (N) Windows 3.1 interface for NCBI IRX server [/pub/software/dos/winirx.uaa to winirx.uae] WINSEQ.UUE (N) Windows version of D. Gilbert's READSEQ (R. Nakisa) [/pub/software/dos/winseq.uue] Mac: ---- ALIGN.HQX (U) Sequence alignments and phylogeny (replacement of corrupt archive) (D. Feng) [/pub/software/mac/align.hqx] AMPLIFY.HQX (U) PCR primer checks v1.2 (B. Engels) [/pub/software/mac/amplify.hqx] BKGCUCLC_FONTS.HQX (N) Color fonts for use with sequence editors (M. Sogin) [/pub/software/mac/bkgcuclc_fonts.hqx] DBCONV.HQX (U) Transformation of line-oriented databases into tab- delimited format v2.0 (J. Valverde) [/pub/software/mac/dbconb.hqx] DIGISPEAK.HQX (N) Sequence reading with sonic digitizer (N. Mantei) [/pub/software/mac/digispeak.hqx] DNAID.HQX (U) DNA sequence editor with grep-like search routine v1.8 (F. Dardel) [/pub/software/mac/dnaid.hqx] EMBL-SEARCH.HQX (U) Database retrieval software for EMBL CD-ROM v2.3.2 (EMBL Data Library) [/pub/software/mac/embl-search.hqx] EMBL-SEARCH_SRC.HQX (U) Source code for EMBL-Search v2.3.2 [/pub/software/mac/embl-search_src.hqx] HTH.C (N) Prediction of helix-turn-helix regions (C. Halling) [/pub/software/mac/hth.c] LABHELPER.HQX (N) General laboratory tools for buffer preps etc. (T. Tzeng) [/pub/software/mac/labhelper.hqx] MACCLADE30_DEMO.HQX (N) Demo of phylogenetic analysis program (W. Maddison) [/pub/software/mac/macclade30_dem From owner-embldatabank@net.bio.net Tue Jul 06 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!uunet!pipex!uknet!pavo.csi.cam.ac.uk!mrc-lmb.cam.ac.uk!rs From: rs@mrc-lmb.cam.ac.uk (Staden R.) Newsgroups: bionet.molbio.embldatabank,bionet.software Subject: Re: Use of sequence library indexes Message-ID: <1993Jul7.135349.4203@infodev.cam.ac.uk> Date: 7 Jul 93 13:53:49 GMT References: <1993Jul1.234108.1@molbiol.ox.ac.uk> <1993Jul2.055206.7673@comp.bioz.unibas.ch> Sender: news@infodev.cam.ac.uk (USENET news) Organization: MRC Laboratory of Molecular Biology, Cambridge UK Lines: 39 Xref: biosci bionet.molbio.embldatabank:204 bionet.software:5395 Nntp-Posting-Host: al.mrc-lmb.cam.ac.uk There have been several articles about the use of indexes for extracting entries from the sequence libraries and the problems that gcg has when an accession number occurs in more than one entry. Mention was made of a package (SRS) that does not have this problem. Readers may be interested to know of our own method of dealing with sequence library indexes (and which also does not suffer from the accession number problem). We decided to use the indexing system that is included on the EMBL cdrom, and using it we can extract entries based on accession number and entry name. In addition we can perform instantaneous author and text searches (the text indexes include every non-trivial word throughout an entry - not just the keywords - so we find it very useful). So this allows us to use EMBL and SWISSPROT from the cdrom (or copied to disk for extra speed), but we also wanted to be able to use EMBL updates and PIR and GenBank. To make this possible we wrote software to create EMBL cdrom style indexes for all libraries ie we create entryname, accession number, author and freetext indexes for all library formats. It is important to realise that we do not change the libraries, but leave them as distributed. Not having to reformat or change the libraries obviously saves a great deal of time and temporary disk space. An article dexcribing the initial work on this subject was buried in Staden,R and Dear,S "Indexing the sequence libraries: software providing a common indexing system for all the standard sequence libraries. DNA Sequence 3, 99-105 (1992). Rodger Staden -- Rodger Staden, Medical Research Council Laboratory Of Molecular Biology, Hills Road, Cambridge, CB2 2QH, ENGLAND Telephone: 0223 402389 Internet: rs@UK.AC.Cam.MRC-LMB Facsimile: 0223 412282 From owner-embldatabank@net.bio.net Wed Jul 07 23:00:00 1993 Path: biosci!U.WASHINGTON.EDU!nok From: nok@U.WASHINGTON.EDU (Supachitra Chadchawan) Newsgroups: bionet.molbio.embldatabank Subject: I would like to know how to submit the sequence to embl-databank. Can anyone tell me, please? Thank you in advance. Message-ID: Date: 8 Jul 93 22:37:26 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 From owner-embldatabank@net.bio.net Sun Jul 18 23:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!usc!howland.reston.ans.net!noc.near.net!uunet!mcsun!sun4nl!news.sara.nl!HASARA11.SARA.NL!A428ENDE From: A428ENDE@HASARA11.SARA.NL Newsgroups: bionet.molbio.embldatabank Subject: Message-ID: <16C10F1D6.A428ENDE@HASARA11.SARA.NL> Date: 19 Jul 93 21:13:58 GMT Organization: S.A.R.A. Academic Computing Services Amsterdam Lines: 8 Nntp-Posting-Host: vm1.sara.nl X-Newsreader: NNR/VM S_1.3.2 Dear Sir, Because I am not familiar with the GCG programs I wrote my own program to parse the feature table of sequences and so tabulate the codon usage in the coding s trand. This works well but I found out that there is a strange discrepancy betw een sequences. About half of them contained in the CDS parameters also the stop codon, but the other half stopped just before the stop codon. Why is this? Henk van de Kamer Email: CHLAMY@SARA.NL From owner-embldatabank@net.bio.net Sun Jul 18 23:00:00 1993 Path: biosci!UUNET.UU.NET!aditya!raman From: aditya!raman@UUNET.UU.NET (K. Ramnarayan) Newsgroups: bionet.molbio.embldatabank Subject: (none) Message-ID: <9307200101.AA03516@aditya> Date: 20 Jul 93 01:01:44 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 5 Hello, I was wondering if anyone knows if any IGG class has been identified for Dolphins? Thanks very much for your help. ..Ramnarayan raman%aditya@uunet.uu.net From owner-embldatabank@net.bio.net Thu Jul 22 23:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!math.ohio-state.edu!uwm.edu!linac!uchinews!kimbark!chh9 From: chh9@kimbark.uchicago.edu (Conrad Halling) Newsgroups: bionet.molbio.embldatabank Subject: Re: Message-ID: <1993Jul23.170509.18779@midway.uchicago.edu> Date: 23 Jul 93 17:05:09 GMT References: <16C10F1D6.A428ENDE@HASARA11.SARA.NL> Sender: news@uchinews.uchicago.edu (News System) Reply-To: chh9@midway.uchicago.edu Organization: University of Chicago Lines: 31 In article <16C10F1D6.A428ENDE@HASARA11.SARA.NL> A428ENDE@HASARA11.SARA.NL writes: >Because I am not familiar with the GCG programs I wrote my own program to >parse the feature table of sequences and so tabulate the codon usage in the >coding strand. This works well but I found out that there is a strange >discrepancy between sequences. About half of them contained in the CDS >parameters also the stop codon, but the other half stopped just before the >stop codon. Why is this? I asked this question myself a few months ago because I, too, have written a program that counts codons. The answer is that EMBL's old definition of the CDS (coding sequence) did NOT include the stop codon. The new standard definition does. Unfortunately, EMBL is behind on fixing the old sequences. Many of these sequences have been transferred to GenBank, so there are some GenBank entries for which the CDS feature does not include the stop codon. The only solution for now is to count the codons, then see if you have a stop codon. If you don't, check the next codon after the end to see if it's a stop codon. As a warning, you will have to check to be sure that there is only one stop codon in a CDS range. You should also check that when you have one stop codon that it is at the end of the CDS range. There are several entries in which the CDS range is incorrect. -- Conrad Halling c-halling@uchicago.edu From owner-embldatabank@net.bio.net Thu Jul 29 23:00:00 1993 Path: biosci!UICVM.UIC.EDU!CAMPALX%BRUFMG From: CAMPALX%BRUFMG@UICVM.UIC.EDU (alex) Newsgroups: bionet.molbio.embldatabank Subject: get sequences Message-ID: <9307302316.AA15088@net.bio.net> Date: 30 Jul 93 23:16:20 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 1 get nuc:M86748 From owner-embldatabank@net.bio.net Thu Jul 29 23:00:00 1993 Path: biosci!UICVM.UIC.EDU!CAMPALX%BRUFMG From: CAMPALX%BRUFMG@UICVM.UIC.EDU (alex) Newsgroups: bionet.molbio.embldatabank Subject: Informations Message-ID: <9307302318.AA15219@net.bio.net> Date: 30 Jul 93 23:18:48 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 17 Dear Sir, I tried to get some informations from this data library at the addres described in the NAR 20 (suppl), 1991. I don't receveive any help and answer,as has been sended. I'm very interested in getting all sequences of Campylobacter and Helicobacter microorganisms. I would like very much if you could send by BITNET the records of this bacteria or a way to get this sequences. Best Regards, Alexandro C. T. Carvalho Department of Microbiology-Instituto de Ciencias Biologicas da UFMG, Belo Horizonte-MG. BRAZIL C.P 2486- 31270-901. FAX 4411412 BITNET CAMPALX@BRUFMG INTERNET CAMPALX@VM1.LCC.UFMG.BR