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In order to use the NetNGlyc server for prediction on amino acid sequences:
  1. Enter a sequence (or multiple sequences in FASTA format) 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.

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

  3. Show additional thresholds: Use this option if you want the graph to include more thresholds than the default 0.5. These additional thresholds (0.32, 0.75, 0.90) are used to assign higher confidence levels for positive and negative sites. See more information in the Output Format notes.

  4. Choose the output format: Predict only on Asparagines that occur within the Asn-Xaa-Ser/Thr triplet, or show output for all Asparagines in the sequence. Note that predictions on Asparagines that do not occur within the Asn-Xaa-Ser/Thr sequon are unlikely to be glycosylated, no matter what the prediction score. The prediction method examines sequence context beyond the Asn-Xaa-Ser/Thr sequon since both the positive and negative data sets only those Asparagines (to train on) that occur in Asn-Xaa-Ser/Thr sequons. See more information in the Output Format notes.

  5. Press the "Submit sequence" button.

  6. 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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