Output format

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

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

1. Sequence ID
2. Type of prediction. Best means the highest scoring class, Margin gives the difference between the best score and the second best score, Class gives the score of other classes and Signal lines contain predicted cleavage sites.
3. Feature type, see below
4. Location in the sequence. For lines with a class prediction it is always 1. For cleavage sites it is the last amino acid of the signal peptide relative to the predicted cleavage site.
5. Location as above axcept that for cleavage sites it is the first amino acids after the cleavage site.
6. Score. For the "Margin" type it is the difference between the best and the second best class score. Otherwise the log-odds score.
7. For the cleavage sites the ±5 context is shown after the #, and for lipoprotein cleavage sites the amino acid in postition +2 is shown (which may determine whether the lipoprotein is attached to the inner or outer membrane, see below).
   

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).

Plot of scores

Below the plot there are links to

• The plot in encapsulated postscript
• A script for making the plot in  gnuplot.