Databases announcement

Amos Bairoch BAIROCH at CMU.UNIGE.CH
Wed Dec 19 05:35:00 EST 1990


Databases release announcement
==============================

The following databases are now available:

- SWISS-PROT release 16.0
- PROSITE release 6.0
- ENZYME release 3.0
- SEQANALREF release 13.5

----------------------------------------------------------------------------

**************
* HIGHLIGHTS *
**************

1) SWISS-PROT release 16.

   Release 16.0  of SWISS-PROT  contains 18364 sequence entries, comprising
   5'986'949 amino  acids abstracted from 17763 references. This represents
   an increase of 9% over release 15.

   We have  finished adding  cross-references to all human protein sequence
   entries  which  are  represented  in  the  latest  edition  of  the  MIM
   (Mendelian Inheritance in Man) book [1].

   [1]  McKusick Victor A.
        Mendelian Inheritance in Man
        Catalogs of autosomal dominant, autosomal recessive, and X-linked
        phenotypes
        Ninth edition
        Johns Hopkins University Press, Baltimore, (1990).


2) PROSITE release 6.0

   PROSITE release 6 contains 375 documentation chapters that describe 433
   different patterns.  Since release 5.1, 77 new chapters have been added
   and 131 have been updated.


3) ENZYME release 3.0

   ENZYME release 3.0 contains information relative to 3071 enzyme entries.
   The data bank is complete and up to date.


4) Databases relationships update

The current status of the relationships between the biomolecular databases is
shown in the following schematic:


                                                        ********************
                        ***********************  <----- * EPD (Promoters)  *
                        *  EMBL Nucleotide    *         ********************
*****************       *  Sequence Data      *
* DMAP          * ----> *  Library            *         ********************
* Drosophila    *       ***********************  <----- * ECD (E. coli)    *
* Genetic map   *                ^  |                   ********************
***************** ------- +      |  |
                          |      |  |
*****************         v      |  v                   ********************
* PROSITE       * <---- ***********************  <----- * ENZYME (EC nom.) *
* (Patterns)    * ----> *  SWISS-PROT         *         ********************
*****************       *  Protein Sequence   *             |
                        *  Data Bank          *             |
*****************       ***********************             v
* REBASE        *         |       |        |            ********************
* (Restriction  * <-------+       |        +--------->  * OMIM  (diseases) *
*  enzymes)     *                 |                     ********************
*****************                 v
                        ***********************
                        * PDB (3D structures) *
                        ***********************

----------------------------------------------------------------------------

****************
* AVAILABILITY *
****************

SWISS-PROT  - On CD-ROM or tape from EMBL (to obtain subscribtion information
              send mail to DATALIB at EMBL.BITNET).
            - Individual entries can be obtained from the EMBL File Server.
            - Will be soon available by FTP from the GenBank On-line Service
              FTP server.

PROSITE     - EMBL File Server.
            - GenBank On-line Service FTP server.
            - NCBI FTP server.
            - On CD-ROM or tape along with SWISS-PROT.

ENZYME      - EMBL File Server.
            - GenBank On-line Service FTP server.
            - NCBI FTP server.
            - On CD-ROM or tape along with SWISS-PROT.

SEQANALREF  - EMBL File Server.
            - GenBank On-line Service FTP server.
            - NCBI FTP server.


a) EMBL File Server

   - Email address: netserv at embl.bitnet

   - To get PROSITE include the following lines in your message:

     get PROSITE:PROSITE.DAT
     get PROSITE:PROSITE.DOC
     get PROSITE:PROSITE.LIS
     get PROSITE:PROSITE.USR

   - To get ENZYME include the following lines in your message:

     get ENZYME:ENZYME.DAT
     get ENZYME:ENZYME.USR

   - To get SEQANALREF include the following lines in your message:

     get REFLIST:SEQANALREF.DAT
     get REFLIST:SEQANALREF.DOC

   - To get an individual SWISS-PROT entry include the following lines in
     your message:

     get PROT:entry_name
     or
     get PROT:ac_numb

     Where entry_name is a SWISS-PROT entry name (example CYC$HUMAN) and
     ac_numb is an accession number (example: P00001).


b) Genbank On-line Service FTP server

   Address: genbank.bio.net (or 134.172.1.160)
   You should login as: user = anonymous
                        password = Your name

   ENZYME files are in    : /pub/db/enzyme
   PROSITE files are in   : /pub/db/prosite
   SEQANALREF files are in: /pub/db/seqanalref

c) NCBI FTP server

   Address: ncbi.nlm.nih.gov (or 130.14.20.1)
   You should login as: user = anonymous
                        password = Your name

   ENZYME files are in    : /repository/ENZYME
   PROSITE files are in   : /repository/PROSITE
   SEQANALREF files are in: /repository/SEQANALREF

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**************
* Newsletter *
**************

A newsletter describing the changes in SWISS-PROT, PROSITE and ENZYME will
be  sent  very  soon  to  the  PROTEIN analysis bulleting board and to all
individual users which have subscribed to the PROSITE newsletter.

This newsletter will now be called GePSAN (Geneva Protein Sequence Analysis
Newsletter).  If  you  were a subscriber to the PROSITE newsletter you will
automatically receive GePSAN. If you were not on the list and you want to be
added to it, you can send mail to:

                 GEPSAN at CGECMU51.BITNET

Note: the previous address PROSITE at CGECMU51 will be dropped in the near
      future, so do not use it anymore.

--------------------------------------------------------------------------
*****************************************************************************
* Amos Bairoch                * Email: bairoch at cgecmu51.bitnet              *
* Dept. Medical Biochemistry  * Tel  : +(41 22) 61 84 92                    *
* CMU                         ***********************************************
* 1, rue Michel Servet        * Ground rule for laboratory workers:         *
* 1211 Geneva 4               * When you don't know what you are doing,     *
* Switzerland                 * do it neatly.                               *
*****************************************************************************





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