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 and X (unknown)

All the other symbols will be converted to X 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 2,000 sequences and 200,000 amino acids in total in one submission. The sequences may not be longer than 4,000 amino acids.

2. Customize your run

• By default the server produces graphical output illustrating the predictions. You can suppress that by un-checking the button labelled 'Generate graphics'.

• Prediction of the presence and location of signal peptide cleavage sites by the SignalP server is included by default. You can suppress that by un-checking the button labelled 'Include signal peptide prediction'.

• Check the button labelled 'Verbose output' to display the scores produced by the 4 individual neural networks alongside the average score. The default is to show the average score only.

• The server performs Furin-specific propeptide cleavage site prediction by default. Check the button labelled 'General PC prediction' to perform that prediction instead.

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.