SignalP

From BioPerl

Contents 1 Description 2 Website 3 Example 3.1 Input 3.2 Output - short 3.3 Output - standard 4 References

Description

SignalP [1, 2, 3] 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

1. Nielsen H, Engelbrecht J, Brunak S, and von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997 Jan; 10(1) 1-6. pmid:9051728. PubMed HubMed [signalp]
2. Nielsen H and Krogh A. Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol 1998; 6 122-30. pmid:9783217. PubMed HubMed [signalphmm]
3. Bendtsen JD, Nielsen H, von Heijne G, and Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004 Jul 16; 340(4) 783-95. doi:10.1016/j.jmb.2004.05.028 pmid:15223320. PubMed HubMed [signalp3]

All Medline abstracts: PubMed HubMed