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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 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, the sequences shorter than 9 or 15 amino acids (depending on the selected prediction options) or longer than 4000 amino acids will be ignored.


2. Customize your run

Under Type of prediction select the prediction type you wish to perform by clicking on the corresponding button. The available types are as follows (see the sequence logos and amino acid table).

Type Limitations

2Apro sites
The network was trained on cleavage sites in entero- and rhinovirus only. Please note that this prediction will only consider potential sites matching the following sequence:

xp3 - xp2 - xp1 * G - xp2' - xp3'

i.e. glycine(G) must be present at position P1'. The 2Apro algorithm has an input window of 15 residues and examines the central residue of this window. This means that the first and last 7 residues of the input sequence will not be processed.

Minimally required sequence (15 aa):

"xxxxxxxxGxxxxxx" (G required, x is any amino acid)


3Cpro sites
(entero+rhino)
The network was trained on cleavage sites in entero- and rhinovirus only. Please note that this prediction will only consider potential sites matching the following sequence:

xp3 - xp2 - Q/E * xp1' - xp2' - xp3'

i.e. glutamine(Q) or glutamic acid(E) must be present at position P1. The 3Cpro algorithm has an input window of 9 residues and examines the central residue of this window. This means that the first and last 4 residues of the input sequence will not be processed.

Minimally required sequence (9 aa):

"xxxx(Q/E)xxxx" (Q or E required)


3Cpro sites
(aphtho)
This network was trained on data from aphthovirus (FMDV). This algorithm was trained to look at all possible input windows of 9 residues and examines the central residue of each such window. This means that the first and last 4 residues of the input sequence will not be processed.

Minimally required sequence (9 aa):

"xxxxxxxxx"


autocatalytic
sites
This network was trained on data from all picornaviruses. Please note that this prediction will only consider potential sites matching the following sequence:

xp3 - L - xp1 * xp1' - xp2' - xp3' - xp4' - E

i.e. leucine(L) must be present at position P2 and glutamic acid(E) must be present at position P5'. The 'auto' algorithm has an input window of 15 residues and examines the central residue of this window. This means that the first and last 7 residues of the input sequence will not be processed.

Minimally required sequence (15 aa):

"xxxxxxLxxxxxExx" (L and E required)


Click on the button labelled "Verbose output" to include the above descriptions in the output.


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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