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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
GETTING HELP
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