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Output format



DESCRIPTION

For each input sequence the following is shown (see the example below):
  • Header line, quoting the name of the sequence.

  • Sequence, in one-letter code, as it was interpreted by the server.

  • List of selected prediction options (see instructions).

  • For each prediction option the output contains predictions for all the input residues matching the pattern for that particular prediction (in the instructions see the notes for each cleavage type). Firstly, a sequential list of the residues is shown and secondly, a list sorted by the value of the cleavage score (highest scores first). For each residue the columns are as follows:

    Residue
    The amino acid residue at position P1 of the cleavage site (P3-P2-P1*P1'-P2'-P3'), where cleavage is between P1 and P1'.
    Pos Position of the residue in your sequence.
    Clv
    Cleavage score output from the neural network in the interval 0.000-1.000. Scores above 0.500 are predicted as potential cleavage sites. The higher the score, the more probable the prediction.
    Surf
    Surface score output from the neural network in the interval 0.000-1.000. Scores above 0.500 are predicted as surface exposed sites. The higher the score, the more probable the prediction.
    Sequence A window of seven residues centered on the residue being examined.
    Comment The word 'Potential' indicates that Clv > 0.500 and the site is a potential cleavage site.

Note: in the output the sequences are sorted alphabetically (by sequence name); thus, the original order is not preserved.


EXAMPLE

Lines containing the prediction scores may look like this:

Residue   Pos   Clv     Surf    Sequence                Comment
-----------------------------------------------------------------
Q          85   0.927   0.626   QNTQGLI                 Potential
E          97   0.077   0.561   NDRERVN



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