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Instructions



In order to use the NetCTL server for prediction on amino acid sequences:
  1. Enter the sequence in the sequence window, or give a file name.

    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. Select HLA supertype (10 HLA supertypes are available)

  3. Optional
    1. Weight on C terminal cleavage. The default select value (0.1) gives optimal predictive performance on average. You can modify the relative weight on proteasomal cleavage by entering a different weight value.
    2. Weight on TAP transport efficiency. The default select value (0.05) gives optimal predictive performance on average. You can modify the relative weight on TAP transport by entering a different weight value.
    3. Threshold for epitope identification. Peptides with a combined prediction score value greater than the threshold value are marked as potential epitopes. In a large scale benchmark identifying known CTL epitope in proteins the default value of 0.75 was found to correspond to a sensitivity of 0.65 and a specificity 0.97. Note that the benchmark is highly unbalanced since only one peptide is identified as CTL epitope in each protein, and the number of negatives hence is orders of magnitude larger than the number of positives. This has important implications for the interpretation of the specificity values.
    4. Sort by score. Select which feature to sort on. Sorting is done in decreasing order. Default is no sorting.

  4. Press the "Submit sequence" button.

  5. A WWW page will return the results when the prediction is ready. Response time depends on system load.



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