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Output format



DESCRIPTION

The output is a table in plain text (see the example below). For each input sequence one table row is output. The columns are as follows:

Name
Sequence name truncated to 20 characters
Len Sequence length
cTP, mTP, SP, other
Final NN scores on which the final prediction is based (Loc, see below). Note that the scores are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class, see below) may be an indication of how certain the prediction is.
Loc Prediction of localization, based on the scores above; the possible values are:
C Chloroplast, i.e. the sequence contains cTP, a chloroplast transit peptide;
M Mitochondrion, i.e. the sequence contains mTP, a mitochondrial targeting peptide;
S Secretory pathway, i.e. the sequence contains SP, a signal peptide;
_ Any other location;
*
"don't know"; indicates that cutoff restrictions were set (see instructions) and the winning network output score was below the requested cutoff for that category.
RC
Reliability class, from 1 to 5, where 1 indicates the strongest prediction. RC is a measure of the size of the difference ('diff') between the highest (winning) and the second highest output scores. There are 5 reliability classes, defined as follows:
    1 : diff > 0.800
    2 : 0.800 > diff > 0.600
    3 : 0.600 > diff > 0.400
    4 : 0.400 > diff > 0.200
    5 : 0.200 > diff
Thus, the lower the value of RC the safer the prediction.
TPlen Predicted presequence length; it appears only when TargetP was asked to perform cleavage site predictions (see instructions).


EXAMPLE OUTPUT

In the example below 12 plant sequences from the Uniprot database have been processed. Cleavage site prediction was enabled; no cutoffs were set. A sequence name longer than 20 characters was truncated.

### targetp v1.1 prediction results ##################################
Number of query sequences:  12
Cleavage site predictions included.
Using PLANT networks.

Name                  Len     cTP    mTP     SP  other  Loc  RC  TPlen
----------------------------------------------------------------------
P11043_has_a_very_ve  516   0.873  0.012  0.004  0.320   C    3     65
P07505                266   0.330  0.047  0.004  0.444   _    5      -
P12360                246   0.580  0.119  0.210  0.089   C    4     42
P12352                 97   0.397  0.555  0.014  0.150   M    5     40
Q01289                399   0.733  0.017  0.031  0.462   C    4     62
P08817                129   0.844  0.092  0.089  0.015   C    2     47
P07263                546   0.400  0.380  0.075  0.020   C    5     41
P07597                117   0.005  0.095  0.967  0.006   S    1     26
P48786               1088   0.199  0.070  0.067  0.822   _    2      -
Q01238                102   0.420  0.277  0.033  0.164   C    5     41
P35334                342   0.055  0.010  0.968  0.041   S    1     29
P13086                333   0.053  0.905  0.045  0.034   M    1     21
----------------------------------------------------------------------
cutoff                      0.000  0.000  0.000  0.000




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