SignalP

Description

SignalP signalp,signalphmm,signalp3 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models.

Website

See http://www.cbs.dtu.dk/services/SignalP/

Example

Input

>MY_PROTEIN_SEQ 
MKSAFSFLPNWPLAPDAIFWAGFALFAAGLCGELCYRAWRLPRITGYAVIGLVAGSFGFGVIDASTDDTSRLLVNVALGL
LLFELGSRLDLRWIRRNPWLIASSLAEATLTFVLVLAVLLLLKVPGMIALVLAAIAISTSPAMVIQLKTELRAEGQVSQR
LITLSALNSVYAVVLTKLVTSWLHQEAYGNVFATILQPIYLLAGSFIVAYLFARACNYLFRHVAATMRDEHSFVALFGLV
VLAIAVAQVLKLSTMLTLLLAGIIVKNLEARPQLWPEHFGTAGWLLTVILFVLTLTSFEGQDIAAGGLIAGALIATRFLA
KLVGVLAFAKPSGLGVKQGIALGVSLVPMSALAYLLVDDTYQLYPNFDPRLRAVVMCSIVVLQLIGPLVVYRSLSAVGER 
RDAS

Output - short

# SignalP-NN gram- predictions                                 	                # SignalP-HMM gram- predictions
# name                Cmax  pos ?  Ymax  pos ?  Smax  pos ?  Smean ?  D     ? 	# name      !  Cmax  pos ?  Sprob ?
MY_PROTEIN_SEQ        0.107  15 N  0.131  28 N  0.912  26 N  0.565 Y  0.348 N	MY_PROTEIN_SEQ  Q  0.028  28 N  0.034 N  

Output - standard

>MY_PROTEIN_SEQ 

SignalP-NN result:

>MY_PROTEIN_SEQ        length = 70
# Measure  Position  Value  Cutoff  signal peptide?
  max. C    15       0.107   0.52   NO
  max. Y    28       0.131   0.33   NO
  max. S    26       0.912   0.92   NO
  mean S     1-27    0.565   0.49   YES
       D     1-27    0.348   0.44   NO
# Most likely cleavage site between pos. 27 and 28: LFA-AG

SignalP-HMM result:

>MY_PROTEIN_SEQ
Prediction: Non-secretory protein
Signal peptide probability: 0.034
Max cleavage site probability: 0.028 between pos. 27 and 28

References

<biblio>

1. signalp3 pmid=15223320
2. signalp pmid=9051728
3. signalphmm pmid=9783217

</biblio>