EMBL File Server News: No. 3, February 12th 1991

NETHELP at embl.bitnet NETHELP at embl.bitnet
Tue Feb 12 10:45:00 EST 1991


------------------------------------------------------------------------------
|  EMBL FILE SERVER News                        Number 3, February 12th 1990 |
|                                                                            |
|  European Molecular Biology Laboratory, Data Library & Computer Group,     |
|  Postfach 10.2209, 6900 Heidelberg, Germany.                               |
|  E-mail: NetHelp at EMBL.bitnet                Tel: +49 6221 387258           |
|          NetHelp at EMBL-Heidelberg.DE         Fax: +49 6221 387519 or 387306 |
------------------------------------------------------------------------------


Contents:

<1> Introduction
<2> Updates to existing data collections
<3> Updates to software collection
<4> Other updates
<5> Summary of contents of file server
<6> Getting started ?

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

    This newsletter and older issues are available from the server (eg. GET
    DOC:EMBL_Server_News.2).


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

    REBase      -  Release 9102 February 1991, of Rich Robert's restriction
                   enzyme database.
    Enzyme      -  Release 3.1 of Amos Bairoch's enzyme database.
    RefList     -  Release 14.0 of Amos Bairoch's SeqAnalRef database.
    TFD         -  Release 2.1 of David Ghosh's transcription factor database

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


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

   DOS:
   ----

   SIM.UUE              (N) Program for detecting local sequence similarities
                            (G. Huang and W. Miller)

   TFD2PROSITE.C        (N) Conversion utility to transform the TFD sites table
                            to Prosite format (R. Fuchs)

   COSY.UAA             (U) Replacing a defect archive on the server.
                            A package for enzyme kinetics calculations
                            (M. Eberhard)

   CREGEX.C             (U) v1.1 of J. Leunissens program to convert Prosite to
                            Prosearch format

   PROSEA12.UAA         (U) v1.2 of L. Kolakowski's program to search patterns
                            in protein sequences using the Prosite database


   Mac:
   ----

   MACTARGSEARCH.HQX    (N) Program to search DNA sequences with sequence
                            profiles (J.A. Goodrich, W.R. McClure, M.L.
                            Schwartz)

   SEQLOGO.HQX          (N) Graphical representation of sequence patterns
                            by "sequence logos" (T. Schneider)

   TFD2PROSITE.C        (N) Conversion utility to transform the TFD sites table
                            to Prosite format (R. Fuchs)

   DNATRANSLATOR.HQX    (U) Update (v.0.97.3) to D.J. Eernisse's HyperCard
                            stack for phylogenetic analyses

   MACPATTERN.HQX       (U) Update (v1.2.3) to R. Fuchs's program for pattern
                            searching using Prosite


   Unix:
   -----

   TFD2PROSITE.C        (N) Conversion utility to transform the TFD sites table
                            to Prosite format (R. Fuchs)

   CREGEX.C             (U) v1.1 of J. Leunissens program to convert Prosite to
                            Prosearch format

   PROSEARCH.UAA        (U) v1.2 of L. Kolakowski's program to search patterns
                            in protein sequences using the Prosite database

   SEQF.UAA             (N) Programs for searching genetic sequence databases
                            (D. Davison and M. Kanehisa)


   VAX:
   ----

   SIM.UUE              (N) Program for detecting local sequence similarities
                            (G. Huang and W. Miller)

   TFD2PROSITE.C        (N) Conversion utility to transform the TFD sites table
                            to Prosite format (R. Fuchs)

   CREGEX.C             (U) v1.1 of J. Leunissens program to convert Prosite to
                            Prosearch format

   PROSEARCH.UAA        (U) v1.2 of L. Kolakowski's program to search patterns
                            in protein sequences using the Prosite database


<4> Other updates
    -------------

    DOC      - BIOSCI.DOC  January 1991 version of the BIOSCI
                           bulletin-board description.
             - GEPSAN.1    Issue 1 of the Geneva Protein Sequence Analysis
                           Newsletter, by Amos Bairoch, University of
                           Geneva
    RefList  - FANS_REF    Functional analysis of nucleotide sequences
                           bibliography, by M.S. Gelfand, USSR Academy of
                           Sciences.


<5> Summary of Directories of the EMBL File Server
    -------------------------------------------

Summary of directories available on the EMBL File Server:

    Databases:

    EMBL Nucleotide Sequence Database                              NUC
      (Rel. 25, Nov 90 + new data from EMBL/GenBank/DDBJ)
    Eukaryotic Promotor Database (Rel. 25, Nov 90)                 EPD
    SwissProt Protein Database (Rel. 16, Oct 90)                   PROT
    ProSite pattern database (Rel. 6.0, Nov 90)                    PROSITE
    ENZYME database (Rel. 3.1, Feb 91)                             ENZYME
    Brookhaven Protein Structure Database (Rel. 54, Nov 90)        PROTEINDATA
    REBASE, Restriction Enzyme Database (Rel. 9102, Feb 91)        REBASE
    TFD, Transcription Factor Database (Ver 2.1, Feb 91)           TFD
    The E.coli Database (Rel. 5, Nov 90)                           ECD
    Drosophila Genetic Map Database (Rel. 3.5, Aug 90)             DROSOPHILA
    Listing of Molecular Biology Databases, LiMB (Rel. 2.0)        LIMB
    Sequence analysis bibliography (SEQANALREF Rel. 14.0, Feb 91)  REFLIST
    Functional Analysis of Nucleotide Sequences bibliography       REFLIST
      (FANS_REF Rel. 1.3, Nov 90)

    Software:

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

    Miscellaneous:

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


<6> Getting Started ?
    -----------------
    The EMBL File Server is a facility available on the EMBL computing system
    for external users to request files by electronic mail. The service is free.

    For initial information, send standard electronic mail to either of the
    addresses:
      NetServ at EMBL.bitnet
      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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