From owner-embldatabank@net.bio.net Thu Jan 07 22:00:00 1993 Path: biosci!TRMETU.BITNET!CONSULT1 From: CONSULT1@TRMETU.BITNET (TAYLAN) Newsgroups: bionet.molbio.embldatabank Subject: NATO ADVANCED STUDY INSTITUTE Message-ID: <9301081246.AA15271@net.bio.net> Date: 8 Jan 93 12:47:28 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 118 Please, distribute to related persons/organizations NATO ADVANCED STUDY INSTITUTE ----------------------------- MOLECULAR ASPECTS OF OXIDATIVE DRUG METABOLIZING ENZYMES AND THEIR SIGNIFICANCE IN ENVIRONMENTAL TOXICOLOGY, CHEMICAL CARCINOGENESIS,AND HEALTH JUNE 20 -- JULY 2 , 1993 KUSADASI-TURKEY ORGANIZED BY: Emel ARINC (TURKEY), Wolfgang KLINGER (GERMANY), John B. SCHENKMAN (USA), John J. STEGEMAN(USA) The primary aim of Institute will be on the recent advances in biochemical, regulatory and molecular aspects of oxidative drug metabolizing enzymes. Mainly cytochrome P450 dependent and Flavin containing monooxygenases will be covered. Significance of these enzymes in genotoxicology, environmental toxicology, chemical car- cinogenesis will be discussed. Therapeutic P450 inhibitors and cytochrome P4501A1 induction in fish and its potential use in bio- chemical monitoring will be considered as special topics of interest. LECTURERS: Richard F. ADDISON (CANADA) Wolfgang KLINGER (GERMANY) Diana ANDERSON (UK) Sergei V. KOTELEVTSEV (RUSSIA) Emel ARINC (TURKEY) David KUPFER (USA) Johannes DOEHMER (GERMANY) Anthony Y.H. LU (USA) Yoshiaki FUJII-KURIYAMA (JAPAN) Franz OESCH (GERMANY) John W. GORROD (UK) Richard M. PHILPOT (USA) Helmut GREIM (GERMANY) John B. SCHENKMAN (USA) Ernest HODGSON (USA) John J. STEGEMAN (USA) Eric F. JOHNSON (USA) Hugo Vanden BOSSCHE (BELGIUM) Chung S. YANG (USA) SESSIONS Session I : BIOCHEMISTRY AND MOLECULAR BIOLOGY OF THE MICROSOMAL CYTOCHROME P450 ISOZYMES Session II : FLAVIN CONTAINING MONOOXYGENASES Session III : METABOLISM AND TOXICITY OF DRUGS AND OTHER XENOBIOTICS Session IV : GENOTOXICOLOGY, PREDICTIVE TESTS, CHEMICAL CARCINOGENESIS AND CYTOTOXICITY Session V : THERAPEUTIC AGENTS AND CYTOCHROME P450 Session VI : ECOTOXICOLOGICAL ASPECTS OF CYTOCHROME P450 AND BIOCHEMICAL MONITORING OF AQUATIC POLLUTANTS Lectures, poster sessions, oral presentations and discussions will be held from 9:00 h. to 12.30 h. and from 16.30 h. till 19:00 h. Approximately 75 participants will be admitted. The Institute is located in a five-star KORUMAR Hotel which has its own beach and Con- ference rooms in KUSADASI, on the Aegean Coast. PARTICIPANTS The Advanced Study Institute will accomodate about 75 graduate stu- dents, post-doctoral fellows and senior scientists from universities, govermental organizations and the industry. Instructions for Applications ------------------------------ Persons wishing to attend the Institute should fill out the enclosed "Application Form" and send it to Director of ASI. Those applying for financial assistance will be required to include a statement giving rea- sons in support of their application and a letter of recommendation from a senior scientist active in the field. Scientific contributions by par- ticipants in poster sessions and in oral presentations (15 min.) are welcome. Abstracts not exceeding one page must be in English. DEADLINE FOR APPLICATION and ABSTRACT SUBMISSION: FEBRUARY 20, 1993 FINANCES: Participants are expected to cover their own travel and living expenses. A limited number of grants covering (part of) these expenses will be available for participants from NATO countries. NO REGISTRATION FEE IS DUE. Upon acceptance, a non-returnible deposit of 100 U.S. dollars will be requested from the successful candidates. Deposits will be reimbursed at the end of the course to the participants. The total cost including half-board, coffe servings, abstract book, and some activities is 550 US dollars per person sharing a double room. Accomodations for the par- ticipiants' family members are available at the same cost as for the participiants . Children at 0-6 years of age will be free of charge. For application forms, write to Dr. Emel ARINC Director of ASI Middle East Technical University ODTU TR 06531 ANKARA-TURKEY Fax: (90) (4) 210 12 79 Telex no: 42761 ODTK TR Tel: (90) (4) 210 10 00 ---> Ext. 3105 For information through E-mail contact Muzaffer TAYLAN CONSULT1@TRMETU.BITNET From owner-embldatabank@net.bio.net Mon Jan 11 22:00:00 1993 Path: biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.molbio.embldatabank Subject: BIOSCI/bionet Frequently Asked Questions Message-ID: <9301121000.AA22340@net.bio.net> Date: 12 Jan 93 10:00:03 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 19 New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheets for BIOSCI. There are two FAQ sheets for the newsgroup system. FAQ I describes the general purpose and uses of the BIOSCI/bionet newsgroups. FAQ II provides details on how to participate in these forums. Both of these FAQs are available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci1.FAQ and pub/BIOSCI/biosci2.FAQ. They may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQs are also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. Sincerely, Dave Kristofferson BIOSCI/bionet Manager kristoff@net.bio.net From owner-embldatabank@net.bio.net Mon Jan 11 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!blitz From: blitz@embl-heidelberg.de Newsgroups: bionet.general,bionet.molbio.embldatabank Subject: MPsrch: announcing a new service. Message-ID: <1993Jan12.175048.63351@embl-heidelberg.de> Date: 12 Jan 93 16:50:48 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 65 Xref: biosci bionet.general:3819 bionet.molbio.embldatabank:134 MPsrch ------ (C) Biocomputing Research Unit, University of Edinburgh, 1992 Smith and Waterman Protein Sequence Database searches on a MasPar MPsrch (by Shane Sturrock and John Collins), the fastest implementation of the exhaustive Best Local Similarity algorithm for Sequence Database searching, is now available through BLITZ, a new e-mail service from the EMBL. MPsrch runs on the 4096-processor MasPar MP-1 machine at the EMBL, using the Smith & Waterman algorithm, performing up to 140,000,000 cell updates per second. Typical search times on the MasPar against Swiss-Prot 23 are: 5037 residues RYNR_RABIT 340 seconds (134,000,000 cell updates/second) 377 " ACTS_HUMAN 40 seconds ( 85,000,000 cell updates/second) To get current help information, e-mail the word HELP in a mail message to the Internet address: Blitz@EMBL-Heidelberg.DE To run a search, using default weight matrix and INDEL cost settings, try sending an e-mail message with the word SEQ on the first line and the sequence in free format on succeeding lines. The end of the sequence is determined either by the end of your mail message, if you do not use an automatic mail signature, or by inserting a new line beginning with the word END. For 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 Help information explains how you can specify a PAM matrix between 1 and 500 PAM's, an INDEL cost and the number of alignments to be returned in the output. The sensitivity of MPsrch depends on the choice of parameters, and searches with default parameter settings alone may not always find the most interesting results. Even with the same query sequence, one set of parameters may find strong alignments best, while a different setting may show up weaker relationships better. Because the search is so fast, we would encourage you to experiment with your own choice of parameter settings. In future developments, we hope to provide searches of other databases, including a nucleotide search facility. John Collins & Shane Sturrock, Des Higgins (Data Library) Biocomputing Research Unit, & Roy Omond (Computer Group) University of Edinburgh, EMBL, Scotland, Heidelberg, U.K. Germany. From owner-embldatabank@net.bio.net Thu Jan 14 22:00:00 1993 Path: biosci!agate!spool.mu.edu!uunet!munnari.oz.au!ariel.ucs.unimelb.EDU.AU!ucsvc.ucs.unimelb.edu.au!lugb!lure.latrobe.edu.au!botbvk From: botbvk@lure.latrobe.edu.au Newsgroups: bionet.molbio.embldatabank Subject: How get a sequence into EMBL databank? Message-ID: <1993Jan15.143953.1@lure.latrobe.edu.au> Date: 15 Jan 93 04:39:53 GMT Sender: news@lugb.latrobe.edu.au (USENET News System) Organization: VAX Cluster, Computer Centre, La Trobe University Lines: 13 Dear Neters, could somebody tell me how to put a sequence into the databank? Where can I get the forms from? and what Email address should I send the sequence to? Is there a particular format for the sequence file? Thanks you in advance Beat von Kanel Department of Botany La Trobe University Bundoora Vic. Australia 3083 Email:botbvk@lure.latrobe.edu.au From owner-embldatabank@net.bio.net Sun Jan 17 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!katerice From: katerice@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: RE: How get a sequence into EMBL databank? Message-ID: <1993Jan18.133454.64532@embl-heidelberg.de> Date: 18 Jan 93 12:34:54 GMT References: <1993Jan15.143953.1@lure.latrobe.edu.au> Organization: EMBL, European Molecular Biology Laboratory Lines: 374 In article <1993Jan15.143953.1@lure.latrobe.edu.au>, botbvk@lure.latrobe.edu.au writes: > Dear Neters, > could somebody tell me how to put a sequence into the databank? > Where can I get the forms from? and what Email address should I send > the sequence to? Is there a particular format for the sequence file? > Thanks you in advance > > Beat von Kanel > Department of Botany > La Trobe University > Bundoora Vic. > Australia 3083 > > Email:botbvk@lure.latrobe.edu.au Dear Beat, Here are some details for submitting to the EMBL database. Submission address is: datasubs@embl-heidelberg.de General address is: datalib@embl-heidelberg.de Update address is: update@embl-heidelberg.de (for updates and notification of publication) FTP address: ftp.embl-heidelberg.de Fileserver: netserv@embl-heidelberg.de There are two main methods of submission. One is to use the Authorin package (from Intelligenetics) for Mac or IBM-PC which we make available by ftp or on our fileserver (see above). The other is to fill out our submission form and append the relevant nucleotide sequence (and amino acid where relevant). I have included the submission form below which includes directions on how best to fill it out. We prefer to have the sequence in GCG format, but any simple format will do. I hope this answers your questions. Please do not hesitate to contact me further. Regards, Kate ----------------------------------------------------------------------------- Kate Rice, EMBL | Post: EMBL Data Library | European Molecular | Biology Laboratory Internet: KateRice@EMBL-Heidelberg.DE | Postfach 10-2209 | D-6900 Heidelberg Phone: +49-6221-387523 | Germany SEQUENCE DATA SUBMISSION FORM This form solicits the information needed for a nucleotide or amino acid sequence database entry. By completing and returning it to us promptly you help us to enter your data in the database accurately and rapidly. These data will be shared among the following databases: DNA Data Bank of Japan (DDBJ; Mishima, Japan); EMBL Nucleotide Sequence Database (Heidelberg, FRG); GenBank (Los Alamos, NM, USA.); National Biomedical Research Foundation Protein Identification Resource (NBRF-PIR; Washington, D.C., USA.); Martinsried Institute for Protein Sequence Data (MIPS; Martinsried, FRG); International Protein Information Database in Japan (JIPID; Noda, Japan) and Swiss-Prot Protein Sequence Database (Geneva, Switzerland and Heidelberg, FRG) Please answer all questions which apply to your data. If you submit 2 or more non-contiguous sequences, copy and fill out this form for each additional sequence. Please include in your submission any additional sequence data which are not reported in your manuscript but which have been reliably determined (for example, introns or flanking sequences). When submitting nucleic acid sequences containing protein coding regions, also include a translation (SEPARATELY from the nucleic acid sequence). Independently sequenced peptides receive Swiss-Prot accession numbers. Then send (1) this form, (2) a copy of your manuscript (if available) and (3) your sequence data (in machine readable form) to the address shown below. Information about the various ways you can send us your data and about formats for the sequence data is given in the following two sections. Thank you. SUBMITTING DATA TO THE EMBL DATA LIBRARY We are happy to accept data submitted in either of the following ways: (1) Electronic file transfer: files can be sent via Internet to: DATASUBS@EMBL-Heidelberg.DE (ask your local network expert for help or phone us). Please ensure that each line in your file is not longer than 80 characters; longer lines often get truncated when they are sent. (2) Floppy disks: we can read Macintosh and IBM- compatible diskettes. Please use the 'save as text only' feature of your editor to save your submission (i.e., in ASCII format), as otherwise we might have difficulty processing it. The EMBL Data Library can be contacted as follows: EMBL Data Library Submissions E-mail DATASUBS@EMBL-Heidelberg.DE Postfach 10.2209 Telefax (+49) 6221 387 519 D-6900 Heidelberg Telephone (+49) 6221 387 258 Federal Republic of Germany When we receive your data we will assign them an accession number, which serves as a reference that permanently identifies them in the database. We will inform you what accession number your data have been given and we recommend that you cite this number when referring to these data in publications. If your manuscript has already been accepted for publication, the accession number can be included at the galley proof stage as a note added in proof. So that we can process your data and inform you of your accession number before you receive the galley proofs, please return this form to us as soon as possible. We suggest that the note added in proof should read approximately as follows: "The nucleotide sequence data reported in this paper will appear in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the accession number(s) ________." FORMATS FOR SUBMITTED DATA We would appreciate receiving the sequence data formatted as follows: Each sequence should include the names of the authors. Each distinct sequence should be listed separately using the same number of bases/residues per line. The length of each sequence in bases/residues should be clearly indicated. Enumeration should begin with a "1" and continue in the direction 5' to 3' (or amino- to carboxy- terminus). Amino acid sequences should be listed using the one-letter code. Translations of protein coding regions in nucleotide sequences should be submitted in a separate computer file from the nucleotide sequences themselves. The code for representing the sequence characters should conform to the IUPAC-IUB standards, which are described in: Nucl. Acids Res. 13: 3021-3030 (1985) (for nucleic acids) and J. Biol. Chem. 243: 3557-3559 (1968) and Eur. J. Biochem 5: 151- 153 (1968) (for amino acids). I. GENERAL INFORMATION ============================================================================== Your last name first name middle initials ------------------------------------------------------------------------------ Institution ------------------------------------------------------------------------------ Address ------------------------------------------------------------------------------ Computer mail address Telex number ------------------------------------------------------------------------------ Telephone Telefax number ============================================================================== On what medium and in what format are you sending us your sequence data? (see instructions at the beginning of this form) [ ] electronic mail [ ] diskette computer: operating system: editor: filename: [ ] magnetic tape (specify format) ============================================================================== II. CITATION INFORMATION ============================================================================== These data represent [ ]new submission [ ]correction (Accession number: ) ============================================================================== These data are [ ] published [ ] in press [ ] submitted [ ] in preparation [ ] no plans to publish ------------------------------------------------------------------------------ authors ------------------------------------------------------------------------------ title of paper ------------------------------------------------------------------------------ journal volume, first-last pages, year ------------------------------------------------------------------------------ Do you agree that these data can be made available immediately? [ ] yes no, they can be made available after: (date) Data published before the stated date will be made available on publication ============================================================================== Does the sequence which you are sending with this form include data that do NOT appear in the above citation? [ ] no [ ] yes, from position _______ to _______ [ ] bases OR [ ] amino acid residues (If your sequence contains 2 or more such spans, use the feature table in section IV to indicate their positions) If so, how should these data be cited in the database? [ ] published [ ] in press [ ] submitted [ ] in preparation [ ] no plans to publish ------------------------------------------------------------------------------ authors ------------------------------------------------------------------------------ address (if different from that given in section I) ------------------------------------------------------------------------------ title of paper ------------------------------------------------------------------------------ journal volume, first-last pages, year ============================================================================== List references to papers and/or database entries which report sequences overlapping with that submitted here. 1st author journal, vol., pages, year and/or database, accession number ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ ============================================================================== III. DESCRIPTION OF SEQUENCED SEGMENT Wherever possible, please use standard nomenclature or conventions. If a question is not applicable to your sequence, answer by writing N.A. in the appropriate space; if the information is relevant but not available, write a question mark (?). ============================================================================== What kind of molecule did you sequence? (check all boxes which apply) [ ] genomic DNA [ ] genomic RNA [ ] cDNA to mRNA [ ] cDNA to genomic RNA [ ] organelle DNA [ ] organelle RNA please specify organelle: [ ] tRNA [ ] rRNA [ ] snRNA [ ] scRNA for viruses: [ ] virus or [ ] provirus or [ ] viroid [ ] DNA or [ ] RNA [ ] ds or [ ] ss or [ ] circular [ ] enveloped or [ ] nonenveloped [ ] other nucleic acid. please specify: [ ] peptide [ ] sequence assembled by [ ] overlap of sequenced fragments [ ] homology with related sequence [ ] other. please specify: [ ] partial: [ ] N-terminal [ ] C-terminal [ ] internal fragment ============================================================================== length of sequence [ ] bases or [ ] amino acids Have you checked for vector contamination? ------------------------------------------------------------------------------ gene name(s) (e.g., lacZ) ------------------------------------------------------------------------------ gene product name(s) (e.g., beta-D-galactosidase) ------------------------------------------------------------------------------ Enzyme Commission number (e.g., EC 3.2.1.23) ------------------------------------------------------------------------------ gene product subunit structure (e.g., hemoglobin alpha-2 beta-2) ============================================================================== The following items refer to the original source of the molecule you have sequenced. If there exists no entry in the database for your organism, please specify further classification details. organism (species) (e.g., Mus musculus) subspecies plant cultivar ------------------------------------------------------------------------------ strain (e.g., K12, BALB/c) substrain ------------------------------------------------------------------------------ name/number of individual/isolate (e.g., patient 123; influenza virus A/PR/8/34) ------------------------------------------------------------------------------ developmental stage [ ] germ line [ ] rearranged ------------------------------------------------------------------------------ haplotype tissue type cell type ------------------------------------------------------------------------------ allele variant [ ] macronuclear ============================================================================== The following items refer to the immediate experimental source of the submitted sequence. name of cell line (e.g., Hela; 3T3-L1) or plant cultivar ------------------------------------------------------------------------------ clone library clone(s), subclone(s) ============================================================================== The following items refer to the position of the submitted sequence in the genome. chromosome (or segment) name/number ------------------------------------------------------------------------------ map position units: [ ] genome % [ ] nucleotide number [ ] other: ============================================================================== Using single words or short phrases, describe the properties of the sequence in terms of: - its associated phenotype(s); - the biological/enzymatic activity of its product; - the general functional classification of the gene and/or gene product - macromolecules to which the gene product can bind (e.g., DNA, calcium, other proteins); - subcellular localization of the gene product; - any other relevant information. - homology (>100bp/30aa) - tissues in which protein/mRNA is expressed ============================================================================== IV. FEATURES OF THE SEQUENCE Please list below the types and locations of all significant features experimentally identified within the sequence. Be sure that your sequence is numbered beginning with "1." Use < or > if a feature extends beyond the beginning or end of the indicated sequence span. In the column marked fill in feature type of feature (see information below) from number of first base/amino acid in the feature to number of last base/amino acid in the feature bp an "x" if numbering refers to position of a base pair in a nucleotide sequence aa an "x" if numbering refers to position of an amino acid residue in a peptide sequence id indicate method by which the feature was identified. E = experimentally; S = by similarity with known sequence or to an established consensus sequence; P = by similarity to some other pattern, such as an open reading frame comp an "x" for a nucleotide sequence feature located on strand complementary to that reported here Significant features include: - regulatory signals (e.g., promoters, attenuators, enhancers) - transcribed regions (e.g., mRNA, rRNA, tRNA). (indicate reading frame if start and stop codons are not present) - regions subject to post-transcriptional modificaton (e.g., introns, modified bases) - translated regions - extent of signal peptide, prepropeptide, propeptide, mature peptide - regions subject to post-translational modification (e.g., glycosylated or phosphorylated sites) - other domains/sites of interest (e.g., extracellular domain, DNA- binding domain, active site, inhibitory site) - sites involved in bonding (disulfide, thiolester, intrachain, interchain) - regions of protein secondary structure (e.g., alpha helix or beta sheet) - conflicts with sequence data reported by other authors - variations and polymorphisms The first 2 lines of the table are filled in with examples. ============================================================================== Numbering for features on submitted sequence [ ] matches manuscript [ ] does not match manuscript ============================================================================== feature from to bp aa id comp ------------------------------------------------------------------------------ EXAMPLE TATA box 276 282 x S ------------------------------------------------------------------------------ EXAMPLE exon 1 301 >382 x ============================================================================== ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ ============================================================================== Be sure to include your sequence in electronic form E8/11.92 (Last change: 15-Dec-1992) From owner-embldatabank@net.bio.net Sun Jan 17 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!gatech!paladin.american.edu!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!news.claremont.edu!nntp-server.caltech.edu!leda.cs.caltech.edu!mikael From: mikael@leda.cs.caltech.edu (Mikael P B Larsson) Newsgroups: bionet.molbio.bio-matrix,bionet.molbio.embldatabank Subject: interactive supercomputing Keywords: interactive supercomputing, computational engineering, Message-ID: <1jedudINNrku@gap.caltech.edu> Date: 18 Jan 93 14:13:33 GMT Organization: California Institute of Technology Lines: 23 Xref: biosci bionet.molbio.bio-matrix:374 bionet.molbio.embldatabank:137 NNTP-Posting-Host: leda.cs.caltech.edu computational biology, computational chemistry Hi, I am working with a new type of high speed logic and its applications for high performance computers. I am particularly interested in "interactive supercomputing". Being an electrical engineer, I have fairly naive views of what people in other disciplines might like to use a strong computer for, so I would be grateful if you could tell me what you are currently using computers for, what tasks you would like to run in interactive mode, where you would like to use models with higher resolution and so on. Pointers to the literature would also be greatly appreciated. Please reply by email. Thanks in advance Mikael Larsson Graduate Student Dept of Computer Science Caltech Pasadena From owner-embldatabank@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!blitz From: blitz@embl-heidelberg.de Newsgroups: bionet.general,bionet.molbio.embldatabank Subject: Swiss-Prot release 24 now on Blitz Message-ID: <1993Jan19.142554.64592@embl-heidelberg.de> Date: 19 Jan 93 13:25:54 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 30 Xref: biosci bionet.general:3879 bionet.molbio.embldatabank:138 Swiss-Prot #24 now available for use with MPsrch on Blitz server. ----------------------------------------------------------------- MPsrch is a program for carrying out similarity searches of protein sequence databases using the best local similarity algorithm of Smith and Waterman. Access to MPsrch is available via an e-mail server: Blitz@EMBL-Heidelberg.DE The server has just been upgraded to provide searches of Swiss-Prot release 24. This is an increase of approximately 5% in terms of the number of sequences and residues, over release 23. Swiss-prot Release Sequences Amino acids 23 26706 9 011 391 24 28154 9 545 427 To get current help information, e-mail the word HELP in a mail message to the Internet address: Blitz@EMBL-Heidelberg.DE John Collins & Shane Sturrock, Des Higgins (Data Library) Biocomputing Research Unit, & Roy Omond (Computer Group) University of Edinburgh, EMBL, Scotland. Heidelberg, Germany. From owner-embldatabank@net.bio.net Mon Jan 18 22:00:00 1993 Path: biosci!embl-heidelberg.de!blitz From: blitz@embl-heidelberg.de Newsgroups: bionet.announce,bionet.general,bionet.molbio.embldatabank Subject: Latest Swiss-Prot now on Blitz Message-ID: Date: 19 Jan 93 13:17:37 GMT Sender: kristoff@net.bio.net Organization: EMBL, European Molecular Biology Laboratory Lines: 30 Approved: bionews-moderator@net.bio.net Xref: biosci bionet.announce:320 bionet.general:3882 bionet.molbio.embldatabank:139 Swiss-Prot #24 now available for use with MPsrch on Blitz server. ----------------------------------------------------------------- MPsrch is a program for carrying out similarity searches of protein sequence databases using the best local similarity algorithm of Smith and Waterman. Access to MPsrch is available via an e-mail server: Blitz@EMBL-Heidelberg.DE The server has just been upgraded to provide searches of Swiss-Prot release 24. This is an increase of approximately 5% in terms of the number of sequences and residues, over release 23. Swiss-prot Release Sequences Amino acids 23 26706 9 011 391 24 28154 9 545 427 To get current help information, e-mail the word HELP in a mail message to the Internet address: Blitz@EMBL-Heidelberg.DE John Collins & Shane Sturrock, Des Higgins (Data Library) Biocomputing Research Unit, & Roy Omond (Computer Group) University of Edinburgh, EMBL, Scotland. Heidelberg, Germany. From owner-embldatabank@net.bio.net Tue Jan 19 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!embl-heidelberg.de!fuchs From: fuchs@embl-heidelberg.de Newsgroups: bionet.molbio.embldatabank Subject: Important change to nucleotide sequence database submission system Message-ID: <1993Jan20.090516.64885@embl-heidelberg.de> Date: 20 Jan 93 08:05:16 GMT Organization: EMBL, European Molecular Biology Laboratory Lines: 66 The international nucleotide sequence database collaboration (DDBJ/EMBL/GenBank) is pleased to announce the following improvement to its submission system. In the past, the editorial policies of several journals required that submitters send their data to one specific databank. As from today, submitters may send their nucleotide sequence data to any of the database groups (DDBJ/EMBL/GenBank) irrespective of the journal in which the data are expected to be published. Any given data set should be submitted to *only* one of the databases. The submitter then need to interact only with this database which in turn will be responsible for sharing the data with the other groups. A primary goal of the submission databases is to present your data to the public at the same time as the sequence appears in print. Therefore, we remind submitters that when they request data to be held in confidence pending publication, they need to inform the databases as soon as possible of the date of the upcoming publication. Researchers who detect a pulished sequence they cannot find in the latest release of the nucleotide sequence databases can also assist in the release of this data by notifying DDBJ, EMBL or Genbank at the addresses shown below. Please use the following addresses for your data submission, general contacts, and update/error reporting: DDBJ: ddbjsub@ddbj.nig.ac.jp (for data submissions) ddbj@ddbj.nig.ac.jp (for other enquiries) ddbjupdt@ddbj.nig.ac.jp (for updates and notification of publication) DNA Data Bank of Japan DNA Research Center, National Institute of Genetics, Mishima, Shizuoka 411, Japan Telephone: +81-559-75-0771 Telefax: +81-559-75-6040 EMBL: datasubs@EMBL-Heidelberg.DE (for data submissions) datalib@EMBL-Heidelberg.DE (for other enquiries) update@EMBL-Heidelberg.DE (for updates and notification of publication) EMBL Data Library, Postfach 10.2209, 6900 Heidelberg, Germany Telephone: +49-6221-387-258 Telefax: +49-6221-387-519 GenBank: gb-sub%life@.lanl.gov (for data submissions) info@ncbi.nlm.nih.gov (for other enquiries) update@ncbi.nlm.nih.gov (for updates and notification of publication) Submissions: GenBank Submissions, Mail Stop K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA Telephone: +1-505-665-2177 Telefax: +1-505-665-3493 Other enquiries: GenBank/NCBI, 8N-803, Bldg. 38A, Bethesda, MD 20894, USA Telephone: +1-301-396-2475 Telefax: +1-301-480-9241 Rainer Fuchs EMBL Data Library Fuchs@EMBL-Heidelberg.DE From owner-embldatabank@net.bio.net Tue Jan 26 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: HABERMANN@AIMP.UNA.AC.AT Newsgroups: bionet.molbio.embldatabank Subject: promotor and database-search? Message-ID: <1993Jan27.182937.12863@gserv1.dl.ac.uk> Date: 27 Jan 93 16:13:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 23 Original-To: embl-db@uk.ac.daresbury X-Vms-To: BITNET"embl-db@daresbury.ac.uk" To the EMBL-DATABANK, bionet.molbio.embldatabank Suppose you had promotor sequences of several - functionally related - genes with a conserved sequence motif in common, 1) how could you find out, if there is already a binding protein known for this specific motif? 2) how would you look for promotors of other genes containing the same conserved sequence element? I know that there exists an Eukaryotic Promotor Database - somewhere out there - which might even be useful. I also heard that this EPD is available on the EMBL-server. Is there any possibility to access this database? If yes, how? If you have any ideas how to solve this problem - apart from performing a fasta with this sequence and looking through the tons of output-datas by hand, we had this idea already and are not thrilled with the thougt, since a fasta-search of about 20 nucleotides against the GenEMBL database overwhelms our imagination - please let me know! Thanks in advance Bianca ----------------------------------------------------------------------------------------------------------------- e-mail address (bitnet) : habermann@aimp.una.ac.at institute of molecular pathology, Dr.Bohrgasse7, A1030 Wien _________________________________________________________________________________ From owner-embldatabank@net.bio.net Wed Jan 27 22:00:00 1993 Path: biosci!agate!spool.mu.edu!darwin.sura.net!fconvx.ncifcrf.gov!fcs260c2!toms From: toms@fcs260c2.ncifcrf.gov (Tom Schneider) Newsgroups: bionet.molbio.embldatabank Subject: Re: promotor and database-search? Message-ID: Date: 28 Jan 93 01:15:57 GMT References: <1993Jan27.182937.12863@gserv1.dl.ac.uk> Sender: usenet@ncifcrf.gov (C News) Distribution: bionet Organization: Frederick Cancer Research and Development Center Lines: 31 Nntp-Posting-Host: fcs260c2.ncifcrf.gov In article <1993Jan27.182937.12863@gserv1.dl.ac.uk> Bianca (HABERMANN@AIMP.UNA.AC.AT) writes: | Suppose you had promotor sequences of several - functionally related - genes | with a conserved sequence motif in common, Two sequence recognizers can have identical consensus sequences, and yet recognize different patterns. Therefore you should not use consensus sequences. Instead, make sequence logos of the sequences you have at hand and compare them to the sequence logos of other sites. The results will be highly sensitive and mathematically much more sensible. See: @article{Stephens.Schneider.Splice, author = "R. M. Stephens and T. D. Schneider", title = "Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites", journal = "J. Mol. Biol.", volume = "228", pages = "1124-1136", year = "1992"} Regards, Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov From owner-embldatabank@net.bio.net Thu Jan 28 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!magnus.acs.ohio-state.edu!zaphod.mps.ohio-state.edu!howland.reston.ans.net!bogus.sura.net!darwin.sura.net!welchgate.welch.jhu.edu!danj From: danj@welchgate.welch.jhu.edu (Dan Jacobson) Newsgroups: bionet.molbio.embldatabank Subject: Re: promotor and database-search? Message-ID: <1993Jan29.161422.17726@welchgate.welch.jhu.edu> Date: 29 Jan 93 16:14:22 GMT References: <1993Jan27.182937.12863@gserv1.dl.ac.uk> Distribution: bionet Organization: Johns Hopkins Univ. Welch Medical Library Lines: 96 In article <1993Jan27.182937.12863@gserv1.dl.ac.uk> HABERMANN@AIMP.UNA.AC.AT writes: >To the EMBL-DATABANK, bionet.molbio.embldatabank > >Suppose you had promotor sequences of several - functionally related - genes with a conserved sequence >motif in common, >1) how could you find out, if there is already a binding protein known for this specific motif? >2) how would you look for promotors of other genes containing the same conserved sequence element? >I know that there exists an Eukaryotic Promotor Database - somewhere out there - which might even be >useful. I also heard that this EPD is available on the EMBL-server. Is there any possibility to access this >database? If yes, how? >If you have any ideas how to solve this problem - apart from performing a fasta with this sequence and >looking through the tons of output-datas by hand, we had this idea already and are not thrilled with the >thougt, since a fasta-search of about 20 nucleotides against the GenEMBL database overwhelms our >imagination - please let me know! >Thanks in advance >Bianca > >----------------------------------------------------------------------------------------------------------------- > >e-mail address (bitnet) : >habermann@aimp.una.ac.at >institute of molecular pathology, Dr.Bohrgasse7, A1030 Wien > >_________________________________________________________________________________ Yes, there is an Euk. Promoter Database (EPD) and you can access it by a variety of ways. If you would like to search the database for keywords or phrases you can search it by gopher. (If you don't know what gopher is write me a note and I'll send you all the information that you need to get it - it's free and on the net). In order to search the EPD Sequence database for keywords point your gopher at merlot.welch.jhu.edu and go to the following directory: --> 12. Search Databases at Welchlab (Cloning Vectors, Euk. Promoters, NRL../ and in that directory read the About-these-searches file and then select --> 4. EPD - Eukaryotic Promoter Database And now search for whatever keywords you'd like - for example to retrieve all the entries on the promoters for heatshock proteins search for heatshock to search for all the promoters for heatshock proteins in Drosophila search for heatshock and drosophila and so on.... If you'd like to retrieve the entire database and use it for a fasta search go back to the top directory and select the following directory: --> 2. FTP Sites For Biology/ and then --> 22. NCBI Repository FTP Archive / and then --> 5. EPD/ and then --> 4. db/ then just select the sequence database: --> 5. epd33.seq. and it will bring it to your system. It's already in Fasta format so just search your promoters against it. Alternately you can retrieve the epd sequence database by anonymous ftp from ncbi.nlm.nih.gov in the /repository/EPD/db/ directory. Best of luck, Dan Jacobson danj@welchgate.welch.jhu.edu Johns Hopkins University From owner-embldatabank@net.bio.net Sun Jan 31 22:00:00 1993 Path: biosci!uwm.edu!cs.utexas.edu!usc!howland.reston.ans.net!paladin.american.edu!news.univie.ac.at!hp4at!mcsun!julienas!genethon!auffray From: auffray@genethon.fr (Charles Auffray) Newsgroups: bionet.molbio.embldatabank,bionet.molbio.genbank.bionet.sci-resources Subject: Declaration_Against_cDNA_Patenting Message-ID: <1993Feb1.115905@genethon.fr> Date: 1 Feb 93 10:59:05 GMT Sender: news@genethon.fr Organization: Genethon -- Human Genome Research Centre Lines: 76 Xref: biosci bionet.molbio.embldatabank:144 Originator: auffray@halogene.genethon.fr Nntp-Posting-Host: halogene.genethon.fr CNRS UPR 420 Laboratoire GENETHON Genetique Moleculaire et Genexpress Biologie du Developpement 1, rue de l'Internationale 7, rue Guy Mocquet BP 8 91002 EVRY cedex 94801 VILLEJUIF cedex FRANCE FRANCE tel. 33 1 69 47 29 65 tel. 33 1 49 58 11 11 fax.33 1 60 77 86 98 fax. 33 1 45 58 11 22 29 January 1993 Dear Colleague, The first part of the catalog of human gene transcripts assembled by the Genexpress cDNA sequencing program (GENETHON, France) has been presented to the French Academie des Sciences by its Secretaire General, Pr. Francois GROS, on 6 July 1992. All these partial cDNA sequences which correspond to unique, previously unidentified sequences are deposited in the EMBL Data Library as they are isolated, and are available for public access as a service to the world scientific community. There are presently 2723 such entries in the EMBL sequence database. In addition, the existing catalog of cDNA sequences was deposited in the hands of UNESCO's Director General, Dr. Federico Mayor, during an official ceremony on 28 October 1992. On this occasion, I expressed the concern of a large number of scientists world-wide concerning attempts to control basic knowledge, and put forward a Declaration, the text of which is attached. All those who wish to express their support of this Declaration are invited to add their name, address and signature to the Declaration and return it to me. The list of signatures collected by the end of February will be published in Nature. Charles AUFFRAY Directeur de Recherche au CNRS Directeur Scientifique Genexpress Laboratoire GENETHON ========================================================================= Declaration to UNESCO - October 28th, 1992 We declare that all basic information derived from the study of the genomes of human, animals, plants and other model organisms (sequences, physical and genetic maps) are part of our human scientific heritage and should therefore be made accessible to the entire scientific community in international electronic databases as soon as possible after their description. We invite all those who hold such data to follow this recommendation and our institutions and governments to enforce and implement it, by law and international agreement if necessary. UNESCO is request to act in order to protect these data against the dangers of monopolization, for the benefit of mankind. Name: Address: Signature: ========================================================================