SWISS-FLASH announcement bulletin.

Amos Bairoch BAIROCH at cmu.unige.ch
Thu May 11 01:20:46 EST 1995


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We are happy to announce the availability of a new service: SWISS-Flash.

SWISS-Flash reports news of  databases, software and services developments
from  the  Swiss  biocomputing  groups  responsible  for  the ECD, ENZYME,
PROSITE, SeqAnalRef, SWISS-2DPAGE, SWISS-3DIMAGE and SWISS-PROT databases;
the Melanie software package; the  ExPASy WWW  and FTP servers; the SWISS-
Model, SWISS-Shop and  other  network-based  computational tools;  and the
SWISS-2DSERVICE services.

By subscribing to this service, you will automatically  get the SWISS-Flash
bulletins by electronic mail. To subscribe you should access the ExPAsy WWW
server (for more info on how to do that, see the last part of this message)
whose address is:

                        http://expasy.hcuge.ch/

or you can directly jump to the relevant page on the server:

                        http://expasy.hcuge.ch/swiss-flash.html


Note: if you have received this message personally by email, it means that
      you are already in the subscription list of Swiss-Flash. You can, of
      course unsubscribe at any time.

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We briefly describe here some of the databases, services, etc which will be
the target of the SWISS-Flash bulletins.


==========
SWISS-PROT
==========

SWISS-PROT is a curated protein sequence database which strives to provide a
high level  of  annotations  (such as the  description of  the function of a
protein, its domains structure, post-translational  modifications, variants,
etc), a minimal level of redundancy and high level of integration with other
databases.

SWISS-PROT was  established in 1986 and is maintained collaboratively, since
1988, by the Department of Medical  Biochemistry of the University of Geneva
and the EMBL European Bioinformatics Institute (EBI) [2].

Release 31.0 of February  1995  contains  43470 sequence entries, comprising
15'335'248 amino acids abstracted  from  39750  references.  The database is
updated weekly  and  the   updates  are  available  on the ExPASy FTP server
(below) or the ExPASy WWW server (see also below).

Reference: Bairoch A., Boeckmann B.
           The SWISS-PROT protein sequence data bank: current status.
           Nucleic Acids Res. 22:3578-3580(1994).


============
SWISS-2DPAGE
============

SWISS-2DPAGE is  a  database   of  proteins  identified  on  two-dimensional
polyacrylamide gel  electrophoresis (2-D PAGE),  created  and  maintained at
the University  Hospital of  Geneva in  collaboration  with  the  Department
of Medical   Biochemistry   of  Geneva  University. The proteins  have  been
identified on   various  2-D  PAGE   reference   maps   by  microsequencing,
immunobloting, gel  comparison  and amino acid composition.  SWISS-2DPAGE is
composed of both text entries and images of gels. It currently contains data
on a variety of human tissues, but an extension of the scope of the database
to cover yeast and Escherichia coli 2-D gels is in preparation.

Reference: Appel R.D., Sanchez J.-C., Bairoch A., Golaz O., Ravier F.,
           Pasquali C., Hughes G.J., Hochstrasser D.F.
           The SWISS-2DPAGE database of two-dimensional polyacrylamide gel
           electrophoresis.
           Nucleic Acids Res. 22:3581-3582(1994).


=============
SWISS-3DIMAGE
=============

SWISS-3DIMAGE is an image  database  which strives  to  provide  high quality
pictures of biological macromolecules with known three-dimensional structure.
The database contains mostly images of experimentally elucidated  structures,
but also provides  views  of  well  accepted  theoretical protein models. The
images are provided in several useful  formats; both mono and stereo pictures
are generally available.

Reference: Peitsch M.C., Wells T.N.C., Stampf D.R., Sussman J.L.
           The Swiss-3DImage collection and PDB-Browser on the World-Wide
           Web.
           Trends Biochem. Sci. 20:82-83(1995).


=======
PROSITE
=======

PROSITE is a method of determining what is the function of uncharacterized
proteins translated  from genomic  or  cDNA  sequences.  It  consists of a
database of  biologically  significant  sites, patterns and  profiles that
help to reliably  identify to which known family of protein (if any) a new
sequence belongs.

Release 12.2  of  February 1995  contains  785  documentation entries that
describe 1029 different patterns, rules and profiles/matrices  that  allow
the characterization of close to 50% of all entries in SWISS-PROT.

Reference: Bairoch A., Bucher P.;
           PROSITE, recent developments.
           Nucleic Acids Res. 22:3583-3589(1994).


======
ENZYME
======

ENZYME is  a repository of information  relative  to  the  nomenclature  of
enzymes. It is primarily based  on the  recommendations of the Nomenclature
Committee of the International Union of Biochemistry  and Molecular Biology
(IUBMB) and it describes each type of characterized enzyme  for which an EC
(Enzyme Commission) number has been provided.

Release 18.0 of February 1995 contains information relative to 3546 enzymes.

Reference: Bairoch A.
           The ENZYME data bank.
           Nucleic Acids Res. 22:3626-3627(1994).


===
EPD
===

EPD provides information about eukaryotic promoters available in the EMBL
Nucleotide  Sequence  Database  and  is  intended  to assist experimental
researchers,  as  well  as  computer  analysts,  in  the investigation of
eukaryotic transcription signals.

Reference: Bucher P., Trifonov E.N.
           Compilation and analysis of eukaryotic POL II promoter sequences.
           Nucleic Acids Res. 14:10009-10026(1986).


==========
SeqAnalRef
==========

SeqAnalRef is a bibliographic reference data bank relative  to papers dealing
with sequence analysis.  This database stores the references of articles from
the expanding field of mathematical  and  computer  analysis  of biomolecular
sequences. The majority of entries belong to one of the following categories:

 - Algorithms for protein  and nucleic acid  sequence  analysis:  primary,
   secondary and tertiary structure analysis; pattern matching; similarity
   searches; alignments, etc.
 - Algorithms for sequence-based phylogenetic analysis.
 - Description of biopolymer data banks:  nucleic acid,  protein, tertiary
   structure, carbohydrates, etc.
 - Description of software packages.
 - Description of on-line services for molecular biologists.

Reference: Bairoch A.
           SEQANALREF: a sequence analysis bibliographic reference data
           bank.
           Comput. Appl. Biosci. 7:268-268(1991).

==========
Melanie II
==========

Melanie II is a workstation based software package for 2-D PAGE analysis. It
automates and  simplifies  the identification, quantitation, and  comparison
of 2-D samples (IPG gels, silver stained gels,  amino-black  PVDF membranes,
phosphorescence plates, autoradiograms).  It  offers  sophisticated analysis
for both single and high volume 2-D comparison studies.

Reference: Appel R., Hochstrasser D.F., Funk M., Vargas J.R., Pellegrini C.,
           Muller A.F., Scherrer J.-R.
           The MELANIE project: from a biopsy to automatic protein map
           interpretation by computer.
           Electrophoresis 12:722-735(1991).


=================
ExPASy WWW server
=================

The ExPASy  WWW server  allows access, using the user-friendly hypertext
model, to  the SWISS-PROT,  PROSITE,  ENZYME,  SWISS-2DPAGE  and  SWISS-
3DIMAGE databases and, through any SWISS-PROT protein sequence entry, to
other  databases   such  as   EMBL,  REBASE,  FlyBase,  GCRDb,  MaizeDB,
SubtiList, OMIM,  PDB, HSSP,  YEPD and Medline. Using a browser which is
able to  display images  one can also remotely access 2D gels image data
from SWISS-2DPAGE.

A WWW  server can  be accessed  on  the  internet  through  its  Uniform
Resource Locator  (URL), the addressing system defined by the WWW model.
The URL for the ExPASy WWW server is:

                        http://expasy.hcuge.ch/

To access a WWW server, you need to run a browser (or client) program on
your local computer. Browsers exist for a variety of machines and may be
obtained by  anonymous ftp. ExPASy can be used with any WWW browser, but
we recommend  either NCSA  Mosaic or  Netscape Navigator.  Both are very
flexible and powerful browsers with a graphical user interface; they are
available for  Unix boxes  using X11/Motif; for Apple McIntoshes and for
Microsoft Windows. You can get them from various FTP sites, for example:

    ftp.ncsa.uiuc.edu (for Mosaic)
    ftp.netscape.com (for Netscape)


Reference: Appel R.D., Bairoch A., Hochstrasser D.F.
           A new  generation of  information retrieval tools for biologists:
           the example of the ExPASy WWW server.
           Trends Biochem. Sci. 19:258-260(1994).


===========
SWISS-Model
===========

Automated protein modelling server.  This  server  allows  you  to  submit  a
protein sequence which the server will then try to align to protein sequences
extracted from PDB. If the alignment is successful, it will launch a software
package, called ProMod that will  automatically build an atomic model for the
query sequence using a knowledge-based approach.

Reference: Peitsch M.C.
           Swiss-Model: an Internet-based comparative protein modelling
           server.
           Bio/Technology  In press(1995).


==========
SWISS-Shop
==========

SWISS-Shop allows any users of SWISS-PROT to indicate what proteins he/she
is  interested in.  This  can  be done by specifying various non-exclusive
criteria  such  as word(s) that should be present in the description line;
species name(s) or taxonomic division(s);  keyword(s);  author name(s); by
entering  the  accession  number (or entry name) of a PROSITE pattern or a
user-defined  sequence  pattern  or  by  entering the accession number (or
entry name) of an existing SWISS-PROT entry or a "private" sequence.

Every  week,  the  new  sequences  entered in SWISS-PROT are automatically
compared with all the criteria that  have  been defined by the users. If a
sequence corresponds to  the  selection  criteria  defined by a user, that
sequence is sent by electronic mail.


=====================
Other WWW based tools
=====================

AACompIdent  allows  the  identification  of a protein  from its  amino acid
             composition. It searches  SWISS-PROT for  proteins, whose amino
             acid  compositions  are  closest to the amino acid  composition
             given.

AACompSim    allows the comparison of the amino acid composition of a SWISS-
             PROT entry with all other SWISS-PROT  entries so as to find the
             proteins whose amino acid compositions  are  closest to that of
             the selected entry.

Comp pI/Mw   allows the computation of the theoretical pI (isolectric point)
             and Mw (molecular weight)  for a given protein stored in SWISS-
             PROT or for a list of SWISS-PROT  entries or for a user entered
             sequence.

GuessProt    allows the retrieval  of  the  SWISS-PROT entries  closest to a
             given pI and Mw.

Translate    allows the translation of a nucleotide (DNA/RNA)  sequence to a
             protein sequence.


=================
ExPASy FTP server
=================

The ExPASy anonymous FTP server address is:

          expasy.hcuge.ch  (or 129.195.254.61)

The following data is currently available on the FTP server:

What                    Where
---------------------   ---------------------------------------------------
SWISS-PROT  rel. 31.0   /databases/swiss-prot
                        /databases/swiss-prot/updates  (Cumulative weekly
                                                        updates)
                        /databases/swiss-prot/special_selections
                                                       (Cumulative subsets)
PROSITE     rel. 12.2   /databases/prosite
ENZYME      rel. 18.0   /databases/enzyme
                        /databases/enzyme/asn          (ASN.1 version)
EPD         rel. 41.0   /databases/epd/db
SEQANALREF  rel. 60.0   /databases/seqanalref
Information files       /databases/info                (See note below [*])

[*] This directory contains a number of documents that describe specific
    organizations;  databases;  email  servers;  FTP servers or software
    packages. See  the  file "listdoc.txt"  for a description of all the
    documents in that directory. It contains, among other documents:

    serv_ftp.txt  List of molecular biology FTP servers for databases
                  and software
    serv_ema.txt  List of molecular biology email servers

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Ron D. Appel                           Amos Bairoch
Unite d'Imagerie Numerique             Dept. Medical Biochemistry
Hopital Cantonal Universitaire         C.M.U.
24, rue Michaeli du Crest              1, rue Michel Servet
1211 Geneva 14                         1211 Geneva 4
Switzerland                            Switzerland

Fax  : +(41 22) 372 61 98              Fax  : +(41 22) 702 55 02
Email: appel at cih.hcuge.ch              Email: bairoch at cmu.unige.ch



Philipp Bucher                         Manuel C. Peitsch
ISREC                                  Glaxo Institute for Molecular Biology
155 ch. des Boveresses                 Ch. des Aulx 14
1066 Epalinges s/Lausanne              1228 Plan les Ouates / Geneva
Switzerland                            Switzerland

Fax  : +(41 21) 652 69 33              Fax  : +(41 22) 794 69 65
Email: pbucher at isrec-sun1.unil.ch      Email: mcp13936 at ggr.co.uk

==========End=of=SWISS-FLASH=announcement bulletin==========================



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