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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)

Non-alphabetic symbols e.g. digits and white space will be ignored. 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 50 sequences in toto in one submission. Sequences longer than 4000 amino acids will be ignored.

NetOGlyc works best on complete protein sequence with signal peptide included. It is possible, however, to submit single sites - you should then include 15 residues on both sides of the Ser/Thr you want evaluated.

2. Customize your run

By default the server produces graphical output illustrating the predictions (in GIF and PostScript). The graphs can be very valuable for locating the "hot" spots in your protein. The generation of graphics can be disabled by un-checking the button labelled 'Generate graphics'.

The signal peptide predictor SignalP is run by default on all the input sequences. A warning is displayed if a signal peptide is not detected. The signal peptide check can be disabled by un-checking the button labelled 'Run signal peptides check'.

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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