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@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. The subject line of the message is ignored. Since this line is echoed back, users may use this line to identify their requests when making more than one. Presently, our automatic server supports the following services: ---------------------------------------------------------------- Help or Info or HelpHelp all Help news 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. Help news send the news about the automatic server. 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. ---------------------------------------------------------------- AllAll IDs, 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"): PamData - get pam distance and variance data PhyloTree, RootedTree - PostScript phylogenetic trees of the sequences SplitData, SplitGraph - isolation indices and graphs 2DPlacement - an approximate 2D placement of the sequences MulAlignment - a multiple alignment of the sequences ProbAncestral - compute the probabilistic ancestral sequence of the sequences KWIndex, ProbIndex, ScaleIndex - variation indices SIAPrediction - Surface/Inside/Active site prediction according to the ETH method ---------------------------------------------------------------- MassSearch DigesterName Weights (the Digester name must be one of the digesters listed in "Help MassSearch", 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. ---------------------------------------------------------------- AllAllDB SelectionExpression (Darwin expression evaluating to boolean) Format OutputClause (printf argument list) Search the all against all database of SwissProt for matches selected by SelectionExpression and output them in the format specified by OutputClause. ---------------------------------------------------------------- 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. ----------------------------------------------------------------
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