Automatic server at ETH Zurich

Gaston Gonnet gonnet at inf.ethz.ch
Tue Dec 1 07:15:59 EST 1992

(Apparently this message never made it to some bionet.software
places, please ignore if you have seen it already).

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.

This server is experimental, and may still have some minor
problems.  If you encounter any difficulty in its operation
we will appreciate your comments/suggestions for improvements.

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 at inf.ethz.ch

Please report problems with the server to

        knecht at 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.  If
    topic is "all", the help file for each function is sent.

    For example (in unix):

        % mail cbrg at inf.ethz.ch
        Help 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.

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.

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>

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

DigestorName Weights (the Digestor 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-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.

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