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.
