[SE] SWISS-FLASH announcement bulletin.
"AmosBairoch"BAIROCH at cmu.unige.ch
"AmosBairoch"BAIROCH at cmu.unige.ch
Thu May 11 01:20:35 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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