From usenet.ucs.indiana.edu!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!mojo.eng.umd.edu!mimsy!biocomp Tue Nov 24 13:15:08 EST 1992
Article: 107 of bionet.biology.computational
Path: usenet.ucs.indiana.edu!sol.ctr.columbia.edu!zaphod.mps.ohio-state.edu!darwin.sura.net!mojo.eng.umd.edu!mimsy!biocomp
From: gonnet@inf.ethz.ch (Gaston Gonnet)
Newsgroups: bionet.biology.computational
Subject: Automatic computational server at ETH, Zurich
Message-ID: <1992Nov24.122753.28317@neptune.inf.ethz.ch>
Date: 24 Nov 92 12:27:53 GMT
Sender: news@mimsy.umd.edu
Distribution: bionet
Organization: Dept. Informatik, Swiss Federal Institute of Technology (ETH), Zurich, CH
Lines: 103
Approved: comp-bio-moderator@genbank.bio.net
Originator: biocomp@lerkim.umiacs.umd.edu

The Computational Biochemistry Research Group (CBRG) at the
ETH in Zurich offers a computing server accessible by e-mail.
Usage is free of charge and open to all researchers who have
access to internet electronic mail.

Queries must be prepared and sent in the appropriate format.
Once processed, the results are returned by e-mail.  Turnaround
time depends upon the load of our machines, the delay of the
electronic mail networks and the complexity of the query.  The
CBRG gives no guarantees, nor assumes any responsibility for
this turnaround time.  All requests will be processed on a
first-come first-served basis.

All the queries submitted to the system are processed with the
Darwin system and publicly available databases.  In general,
these results could be reproduced by any user who obtains
a copy of Darwin and a copy of the databases.  Darwin is also
distributed without charge by the CBRG.

Requests should be mailed to

        cbrg@inf.ethz.ch

Please report problems with the server to

        knecht@inf.ethz.ch

The first line of any request should contain the requested
service.  Each e-mail message can only contain one request.
Presently, our automatic server supports the following services:

----------------------------------------------------------------
Help or
Info or
Help <topic>

    This file, or when a service name is specified as a topic,
    more detailed information on that particular request.

    For example (in unix):

        % mail cbrg@inf.ethz.ch
        Help PepPepSearch
        .
        EOT

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

PepPepSearch
AminoAcidSequence (may be in several lines)

    Search the given amino acid sequence against the entire
    SwissProt peptide database using Smith-Waterman's version
    of dynamic programming.
----------------------------------------------------------------

NuclPepSearch
NucleotideSequence (may be in several lines)

    Search the given nucleotide sequence directly against the
    entire SwissProt peptide database using the algorithm by
    Knecht and Gonnet.
----------------------------------------------------------------

PepNuclSearch
PeptideSequence (may be in several lines)

    Search the given amino acid sequence directly against the
    entire EMBL nucleotide database using the algorithm by
    Knecht and Gonnet.
    <not available until later this year>
----------------------------------------------------------------

AllAll
AccessionNumbers and sequences (separated by commas, terminate with ".")
Commands        (one or many, separated by commas or spaces)

    Do an all-against-all of the given sequences and use these
    results to do (requested by "Commands"):
        PhyloTree - a postcript phylogenetic tree of the sequences
        2DPlacement - an approximate 2D placement of the sequences
        MulAlignment - a multiple alignment of the sequences
        ProbAncestor - compute the probabilistic ancestral sequence
                        of the sequences
----------------------------------------------------------------

MassSearch
DigesterName Weights (the Digester name is either Trypsin or AspN,
                      the weights are numbers separated by spaces
                      or commas)

    Search the SwissProt database for sequences which when digested
    by the given enzyme will match the given set of weights.
    (not available until later this year)
----------------------------------------------------------------

Darwin
Darwin-commands  (a program or as many commands as desired)

    Run the given Darwin commands.  The user is completely responsible
    for the syntax and semantics of the program.
----------------------------------------------------------------