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)
The characters not in the one-letter amino acid code e.g. letters like
'B' or 'Z', digits and other non-alphabetic symbols will all be
converted to X before processing; they will be accepted but not used
when making the predictions. White space within the sequences, if any, will be
ignored. The sequences can be input in the following two ways:
- Paste a single sequence or several sequences in
format into the input field.
Note: if you paste more than one sequence FASTA format must be
- Submit a file in FASTA format
directly from your local disk. The file may contain multiple sequences.
Both methods may be used in the same submission. Peptides shorter than
9 residues can produce non-reliable results. Always include 4 residues on both
sides of the Tyr/Ser/Thr you want evaluated. The optimal is to use the complete
"native" protein sequence.
2. Customize your run
By default the server predicts phosphorylation sites for all the serine,
threonine and tyrosine residues in the input sequences, displays all the
predictions made for each such residue and generates graphical output
illustrating the results. These settings can be changed, as follows:
- "Residues to predict" - the scope of prediction can be limited to
just one of serine/threonine/tyrosine. The deafult is to predict for all the
three amino acids.
- "For each residue display only the best prediction" - for each
residue the server can be made to display only the prediction with the highest
score. The default is to display all the predictions for all the residues.
- "Display only the scores higher than ..." - only the predictions
with scores higher than a given threshold will be displayed. By default all
the predictions are displayed (the threshold of "0"). NOTE: the choice of
"0.5" will imply that only the positive predictions will be shown (see
the Output format).
- "Output format" - by default the output format is the native NetPhos
format (see the Output format). It can be changed to GFF.
- "Generate graphics" - by default the server produces graphical
output illustrating the predictions. This can be disabled.
Before sumitting larger runs, the user is advised to test the settings above
on a few sequences, to arrive at the best combination for a given run.
3. Submit the job
When ready press the button labelled 'Submit
'. 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.