The output format is essentially in GFF format. The default (long) output format looks like this:
# ANIA_NEIGO SpII score=29.6052 margin=11.2327 cleavage=18-19 Pos+2=G # Cut-off=-3 ANIA_NEIGO LipoP1.0:Best SpII 1 1 29.6052 ANIA_NEIGO LipoP1.0:Margin SpII 1 1 11.2327 ANIA_NEIGO LipoP1.0:Class SpI 1 1 18.3725 ANIA_NEIGO LipoP1.0:Class CYT 1 1 -0.200913 ANIA_NEIGO LipoP1.0:Signal CleavII 18 19 29.6052 # FALAA|CGGEQ Pos+2=G ANIA_NEIGO LipoP1.0:Signal CleavI 24 25 18.0333 # GGEQA|AQAPA ANIA_NEIGO LipoP1.0:Signal CleavI 20 21 15.9259 # LAACG|GEQAA ANIA_NEIGO LipoP1.0:Signal CleavI 26 27 12.0794 # EQAAQ|APAET ANIA_NEIGO LipoP1.0:Signal CleavI 25 26 11.4077 # GEQAA|QAPAE ANIA_NEIGO LipoP1.0:Signal CleavI 27 28 9.40252 # QAAQA|PAETP(output trunctated)
The first line, which is the only line if short
output is chosen, summarizes the best prediction. In the example the
best prediction is a lipoprotein with a cleavage site between amino acid
18 and 19 and amino acid G (glycine) in position +2 after the cleavage site.
The second line gives the cut-off used. In the following the columns contain
These 4 clases are predicted
SpI: signal peptide (signal peptidase I)
SpII: lipoprotein signal peptide (signal peptidase II)
TMH: n-terminal transmembrane helix. This is generally not a very reliable prediction and should be tested. This part of the model is mainly there to avoid tranmembrane helices being falsely predicted as signal peptides.
CYT: cytoplasmic. It really just means all the rest.
For technical reasons (see paper) the score for CYT is always the same.
These signals are predicted:
CleavI: Cleavage sites for (signal peptidase I).
CleavII: Cleavage sites for (signal peptidase II).
Below the plot there are links to
Correct class |
Predicted class |
||||
SPaseI |
SPaseII |
Cytoplasmic |
TMH |
Total |
|
SPaseI |
309 |
2 |
14 |
3 |
328 |
SPaseII |
2 |
61 |
0 |
0 |
63 |
Cytoplasmic |
5 |
1 |
382 |
0 |
388 |
TMH |
8 |
0 |
21 |
142 |
171 |