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Usage instructions


1. Specify the input sequences

All the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:

A C D E F G H I K L M N P Q R S T V W Y

Please note that the sequences containing other symbols e.g. X (unknown) will be discarded before processing. The sequences can be input in the following two ways:

  • Paste a single sequence (just the amino acids) or a number of sequences in FASTA format into the upper window of the main server page.

  • Select a FASTA file on your local disk, either by typing the file name into the lower window or by browsing the disk.

Both ways can be employed at the same time: all the specified sequences will be processed. However, there may be not more than 10 sequences in toto in one submission.

The sequences shorter than 15 or longer than 4000 amino acids will be ignored.


2. Select the output format

By default the server only shows the final protein function predictions.
  • If you select the option "Show the individual features ... in the output" the the output of the individual feature prediction servers used by ProtFun (signal peptide and propeptide cleavage sites, other post-translational and localizational aspects of the protein etc.) will be included in the output.

    Note:   At present (Mar 20, 2004) we only show the output of the prediction methods created at CBS. In near future we hope to be able to show all the individual feature predictions used by ProtFun.

  • If you select the option "Show the prediction process as it progresses" the progress of the prediction process will be reported in detail.


3. Submit the job

Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.

At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.

NOTE: ProtFun is dependent on a number of other programs that have to be run on the input sequences prior to employing the ProtFun method itself. Therefore, the processing of multiple sequences may be time-consuming. In the case of prolonged wait the user is advised to use the e-mail option mentioned above.


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