Instructions

In order to use the YinOYang WWW server for prediction on amino acid sequences:

1. (optional) Enter a name for the sequence.

2. Enter a single sequence (or a Swissprot ID or AC) in the sequence window. Alternatively, give a file name containing sequences in FASTA format (multiple sequences allowed).

   The sequence must be written using the one letter amino acid code: `acdefghiklmnpqrstvwy' or `ACDEFGHIKLMNPQRSTVWY'.
   Other letters will be converted to `X' and treated as unknown amino acids.
   Other characters, such as whitespace and numbers, will simply be ignored.

3. Choose the output format: Show only positive predictions, or show potentials for all Ser/Thr sites in the sequence(s).

4. Include Graph: A graphic illustrating glycosylation potentials across the sequence length will be generated (recommended).

5. "Yin-yang" site predictions: Checking this box will (in parallel) generate predictions from the NetPhos server and will indicate Ser/Thr sites which have a potential for being O-GlcNAcylated as well as phosphorylated ('yin-yang' sites). The graphic is affected accordingly.

6. NetPhos threshold: This may be adjusted (0-1, default: 0.5). Sites are indicated as phosphorylated only if their NetPhos potentials are above this fixed threshold.

7. Press the "Submit sequence" button.

8. A WWW page will return the results when the prediction is ready. Response time depends on system load, but is usually only a few seconds.

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