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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

All the other symbols will be converted to A (alanine) 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 2000 sequences in toto in one submission. The sequences shorter than 10 or longer than 6000 amino acids will be ignored.


2. Customize your run

  • Select the threshold for epitope assignment
    The residues with scores above the threshold will be predicted to be part of an epitope and marked with "E" in the server output. The values of the scores are not affected by the selected threshold.

    The default threshold is 0.35; it is usually sensible to make a test run using that value. The guidelines for threshold setting can be found in the output format description.


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.




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