EMBL File Server News No. 4, March 21st 1991

Mon Mar 25 04:13:00 EST 1991

|  EMBL FILE SERVER News                           Number 4, March 21st 1991 |
|                                                                            |
|  European Molecular Biology Laboratory, Data Library & Computer Group,     |
|  Postfach 10.2209, 6900 Heidelberg, Germany.                               |
|                                             Tel: +49 6221 387258           |
|  E-mail: NetHelp at EMBL-Heidelberg.DE         Fax: +49 6221 387519 or 387306 |


<1> Introduction
<2> Updates to data collections
<3> Updates to software collection
<4> Other updates
<5> Common questions
<6> Summary of contents of file server
<7> Notice of EMBL's withdrawal from Bitnet
<8> Getting started ?

<1> Introduction
    The EMBL File Server Newsletter summarises changes to the EMBL File Server.

    This newsletter and older issues are available from the server (eg. GET

<2> Updates to Data Collections
    The following data collections have been updated recently:

    Nuc         -  Release 26, February 1991, of the EMBL Nucleotide Sequence
    Prot        -  Release 17, February 1991, of the SWISS-PROT Protein Sequence
    ProteinData -  A database of homology-derived protein structures (HSSP)
                   supplied by Chris Sander is now available along with the
                   existing Brookhaven PDB and the DSSP secondary structure
                   digest of the PDB protein files.
    ProSite     -  Release 6.1 of Amos Bairoch's pattern database.
                   A version of ProSite suitable for use with Scrutineer is
                   now available.
    Enzyme      -  Release 4 of Amos Bairoch's enzyme database.
    ECD         -  Release 6 of Manfred Kroeger's E.coli database
    Reflist     -  Release 15 of Amos Bairoch's sequence analysis bibliography.
    ReBase      -  Release 9103 of Rich Roberts's restriction enzyme database.
    Alu         -  Jerzy Jurka's Alu Sequence Database, October 1988

    The directory NUC is continually updated with nucleotide sequence data
    from EMBL/GenBank/DDBJ, and the directory PROT is updated with data
    from the SWISS-PROT protein sequence database.

<3> Updates to Software Collection
    Here is a list of new (N) molecular biological programs or updates (U):


    EASISTAT.UAA        (N) Statistical analysis package (D. Curtis)
    PEDRAW.UAA          (N) Pedigree drawing (D. Curtis)


    MATMETH.HQX         (U) New version 5.0 of Material & Methods stack
                            J. Brown
    MACREVIEW.1         (N) Two reviews of Mac software in molecular biology
    MACREVIEW.2             (P. Markiewicz)


    SEQF.UAA            (N) Package for searching genetic sequence libraries
                            (D. Davison and M. Kanehisa)


    SCRUTINE.UAA        (U) New version of SCRUTINEER protein database
                            analysis package (P. Sibbald)
    CDACCESS.UAA        (U) Update (v2.06) of CD-ROM access software
                            (P. Stockwell)

<4> Other updates

    DOC        - BIOSCI.DOC  March 1991 version of the BIOSCI
                             bulletin-board description.
               - SERVER.TXT  Michael Gribskov's Molecular Biology FTP and
                             Server List, March 7th 1991.
               - BIOBIT.19   Rob Harper's newletter, BioBit No. 19: "Archie"

    ALIGN      - DS6748.UUE  Alignment of germline VH gene sequences, submitted
                             by W. Mueller, 6-Mar-1991.

    CODONUSAGE - A collection of codon usage tables in GCG format provided by
                 Mike Cherry.

<4> Common questions

    Q: Can I access the EMBL File Server via FTP ?

    A: Not yet. We are on Internet and await an upgrade to our connection
       before starting an anonymous ftp service.

<6> Summary of Directories of the EMBL File Server


    EMBL Nucleotide Sequence Database                              NUC
      (Rel. 26, Feb 91 + new data from EMBL/GenBank/DDBJ)
    Eukaryotic Promotor Database (Rel. 26, Feb 91)                 EPD
    SwissProt Protein Database (Rel. 17, Feb 91)                   PROT
    Prosite pattern database (Rel. 6.1, Feb 91)                    PROSITE
    ENZYME database (Rel. 4, Feb 91)                               ENZYME
    Brookhaven Protein Structure Database (Rel. 54, Nov 90)        PROTEINDATA
    REBASE, Restriction Enzyme Database (Rel. 9103, Mar 91)        REBASE
    TFD, Transcription Factor Database (Ver 2.1, Feb 91)           TFD
    The E.coli Database (Rel. 6, Feb 91)                           ECD
    Drosophila Genetic Map Database (Rel. 9012, Dec 90)            DROSOPHILA
    Listing of Molecular Biology Databases, LiMB (Rel. 2.0)        LIMB
    Sequence analysis bibliography (SEQANALREF Rel. 15, Feb 91)    REFLIST
    Functional Analysis of Nucleotide Sequences bibliography       REFLIST
      (FANS_REF Rel. 1.3, Nov 90)
    Alu sequence database and alignment                            ALU


    Software for MS-DOS computers                                  DOS_SOFTWARE
    Software for Apple Macintosh                                   MAC_SOFTWARE
    Software for UNIX                                              UNIX_SOFTWARE
    Software for VAX/VMS                                           VAX_SOFTWARE
    Other software, GenBank Clearinghouse, etc.                    MISC_SOFTWARE


    Technical documents, submission and order forms, etc.          DOC
    Multiple DNA sequence alignments and consensus sequences       ALIGN
    Codon Usage tables                                             CODONUSAGE

<7> Notice of EMBL's withdrawal from Bitnet
    EMBL intends to withdraw from Bitnet as from January 1st 1992. The network
    address EMBL.Bitnet should function up until that date, but we recommend
    that users switch to using EMBL-Heidelberg.DE (Internet) from now onwards.

<8> Getting Started ?
    The EMBL File Server is a facility available on the EMBL computing system
    for external users to request files by electronic mail. The service is free.

    For initial information, send standard electronic mail to the address:
      NetServ at EMBL-Heidelberg.DE
    containing just the word HELP on a line by itself. No essays please.
    For human contact, send electronic mail to NetHelp at the address(es)
    given above.

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