BAIROCH@CMU.UNIGE.CH (Amos Bairoch) (12/19/90)
Databases release announcement
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The following databases are now available:
- SWISS-PROT release 16.0
- PROSITE release 6.0
- ENZYME release 3.0
- SEQANALREF release 13.5
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* HIGHLIGHTS *
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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) *
***********************
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* AVAILABILITY *
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SWISS-PROT - On CD-ROM or tape from EMBL (to obtain subscribtion information
send mail to DATALIB@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@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 *
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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@CGECMU51.BITNET
Note: the previous address PROSITE@CGECMU51 will be dropped in the near
future, so do not use it anymore.
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* Amos Bairoch * Email: bairoch@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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