esignalp

 

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Function

Reports protein signal cleavage sites

Description

SignalP 3.0 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.

Usage

Here is a sample session with esignalp 


% esignalp 
Reports protein signal cleavage sites
Input (aligned) sequence set: test.seq
Organism
       euk : euk
     gramp : gram positive
     gramn : gram negative
Organism type to use [euk]: 
Algorithm method
    nn+hmm : Neural net plus hmm
        nn : Neural net
       hmm : Hmm
Method to use [nn+hmm]: 
Text output format
      full : Full
   summary : Summary
     short : Short
Output format [full]: 
Graphics mode
      none : none
       gif : gif
       eps : eps
   gif+eps : gif+eps
        ps : ps
Graphics output [none]: 
       1.0 : 1.0
       1.1 : 1.1
       2.0 : 2.0
       3.0 : 3.0
Signalp version weights [3.0]: 
Output file [test.esignalp]:

Go to the input files for this example
Go to the output files for this example

Command line arguments 

Reports protein signal cleavage sites
Version: EMBOSS:6.3.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) sequence set filename and optional
                                  format, or reference (input USA)
   -type               menu       [euk] Organism type to use (Values: euk
                                  (euk); gramp (gram positive); gramn (gram
                                  negative))
   -method             menu       [nn+hmm] Method to use (Values: nn+hmm
                                  (Neural net plus hmm); nn (Neural net); hmm
                                  (Hmm))
   -format             menu       [full] Output format (Values: full (Full);
                                  summary (Summary); short (Short))
   -gmode              menu       [none] Graphics output (Values: none (none);
                                  gif (gif); eps (eps); gif+eps (gif+eps); ps
                                  (ps))
   -synver             menu       [3.0] Signalp version weights (Values: 1.0
                                  (1.0); 1.1 (1.1); 2.0 (2.0); 3.0 (3.0))
  [-outfile]           outfile    [*.esignalp] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -truncate           integer    [0] Truncate sequence to n N-terminal
                                  residues (0=off) (Integer 0 or more)
   -keepall            boolean    [N] Keep all gnuplot files

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)		 seqset (Aligned) sequence set filename and optional format, or reference (input USA) Readable set of sequences Required
-type list Organism type to use
euk (euk)
gramp (gram positive)
gramn (gram negative)
 euk
-method list Method to use
nn+hmm (Neural net plus hmm)
nn (Neural net)
hmm (Hmm)
 nn+hmm
-format list Output format
full (Full)
summary (Summary)
short (Short)
 full
-gmode list Graphics output
none (none)
gif (gif)
eps (eps)
gif+eps (gif+eps)
ps (ps)
 none
-synver list Signalp version weights
1.0 (1.0)
1.1 (1.1)
2.0 (2.0)
3.0 (3.0)
 3.0
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.esignalp
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-truncate integer Truncate sequence to n N-terminal residues (0=off) Integer 0 or more 0
-keepall boolean Keep all gnuplot files Boolean value Yes/No No
Associated qualifiers
"-sequence" associated seqset qualifiers
-sbegin1
-sbegin_sequence		 integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence		 integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence		 boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-sdbname1
-sdbname_sequence		 string Database name Any string  
-sid1
-sid_sequence		 string Entryname Any string  
-ufo1
-ufo_sequence		 string UFO features Any string  
-fformat1
-fformat_sequence		 string Features format Any string  
-fopenfile1
-fopenfile_sequence		 string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

esignalp reads any normal sequence USAs.

Input files for usage example

File: test.seq

>14KD_DAUCA
MGSKNSASVALFFTLNILFFALVSSTEKCPDPYKPKPKPTPKPTPTPYPSAGKCPRDALK
LGVCADVLNL

Output file format

Output files for usage example

File: test.esignalp

*********************** SignalP 3.0 predictions ***********************
Using neural networks (NN) and hidden Markov models (HMM) trained on eukaryotes

----------------------------------------------------------------------
>14KD_DAUCA

SignalP-NN result:
>14KD_DAUCA            length = 70

# pos  aa    C       S       Y
    1   M   0.008   0.666   0.000
    2   G   0.008   0.759   0.000
    3   S   0.008   0.594   0.000
    4   K   0.008   0.583   0.000
    5   N   0.008   0.652   0.000
    6   S   0.008   0.700   0.000
    7   A   0.008   0.662   0.000
    8   S   0.008   0.861   0.000
    9   V   0.008   0.859   0.000
   10   A   0.008   0.891   0.000
   11   L   0.008   0.895   0.000
   12   F   0.011   0.628   0.000
   13   F   0.008   0.916   0.000
   14   T   0.008   0.922   0.000
   15   L   0.009   0.837   0.000
   16   N   0.008   0.910   0.000
   17   I   0.009   0.969   0.024
   18   L   0.009   0.982   0.038
   19   F   0.010   0.965   0.051
   20   F   0.013   0.958   0.067
   21   A   0.028   0.925   0.110
   22   L   0.049   0.906   0.158
   23   V   0.026   0.925   0.123
   24   S   0.023   0.919   0.121
   25   S   0.049   0.924   0.188
   26   T   0.681   0.826   0.731
   27   E   0.304   0.350   0.511
   28   K   0.054   0.291   0.214
   29   C   0.178   0.070   0.381
   30   P   0.029   0.041   0.150
   31   D   0.063   0.032   0.211
   32   P   0.009   0.017   0.077
   33   Y   0.017   0.014   0.099
   34   K   0.011   0.010   0.076
   35   P   0.008   0.009   0.061
   36   K   0.027   0.013   0.100
   37   P   0.008   0.013   0.049
   38   K   0.009   0.013   0.046
   39   P   0.008   0.011   0.037
   40   T   0.008   0.003   0.030


  [Part of this file has been deleted for brevity]

   26   T   0.704   0.281   0.000   0.001   0.281
   27   E   0.280   0.001   0.000   0.000   0.001
   28   K   0.000   0.001   0.000   0.000   0.001
   29   C   0.000   0.001   0.000   0.000   0.001
   30   P   0.000   0.001   0.000   0.000   0.001
   31   D   0.001   0.000   0.000   0.000   0.000
   32   P   0.000   0.000   0.000   0.000   0.000
   33   Y   0.000   0.000   0.000   0.000   0.000
   34   K   0.000   0.000   0.000   0.000   0.000
   35   P   0.000   0.000   0.000   0.000   0.000
   36   K   0.000   0.000   0.000   0.000   0.000
   37   P   0.000   0.000   0.000   0.000   0.000
   38   K   0.000   0.000   0.000   0.000   0.000
   39   P   0.000   0.000   0.000   0.000   0.000
   40   T   0.000   0.000   0.000   0.000   0.000
   41   P   0.000   0.000   0.000   0.000   0.000
   42   K   0.000   0.000   0.000   0.000   0.000
   43   P   0.000   0.000   0.000   0.000   0.000
   44   T   0.000   0.000   0.000   0.000   0.000
   45   P   0.000   0.000   0.000   0.000   0.000
   46   T   0.000   0.000   0.000   0.000   0.000
   47   P   0.000   0.000   0.000   0.000   0.000
   48   Y   0.000   0.000   0.000   0.000   0.000
   49   P   0.000   0.000   0.000   0.000   0.000
   50   S   0.000   0.000   0.000   0.000   0.000
   51   A   0.000   0.000   0.000   0.000   0.000
   52   G   0.000   0.000   0.000   0.000   0.000
   53   K   0.000   0.000   0.000   0.000   0.000
   54   C   0.000   0.000   0.000   0.000   0.000
   55   P   0.000   0.000   0.000   0.000   0.000
   56   R   0.000   0.000   0.000   0.000   0.000
   57   D   0.000   0.000   0.000   0.000   0.000
   58   A   0.000   0.000   0.000   0.000   0.000
   59   L   0.000   0.000   0.000   0.000   0.000
   60   K   0.000   0.000   0.000   0.000   0.000
   61   L   0.000   0.000   0.000   0.000   0.000
   62   G   0.000   0.000   0.000   0.000   0.000
   63   V   0.000   0.000   0.000   0.000   0.000
   64   C   0.000   0.000   0.000   0.000   0.000
   65   A   0.000   0.000   0.000   0.000   0.000
   66   D   0.000   0.000   0.000   0.000   0.000
   67   V   0.000   0.000   0.000   0.000   0.000
   68   L   0.000   0.000   0.000   0.000   0.000
   69   N   0.000   0.000   0.000   0.000   0.000
   70   L   0.000   0.000   0.000   0.000   0.000
>14KD_DAUCA
Prediction: Signal peptide
Signal peptide probability: 0.990
Signal anchor probability: 0.008
Max cleavage site probability: 0.704 between pos. 25 and 26

Data files

None.

Notes

None.

References

Locating proteins in the cell using TargetP, SignalP, and related tools Olof Emanuelsson, Søren Brunak, Gunnar von Heijne, Henrik Nielsen Nature Protocols 2, 953-971 (2007).

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
antigenic Finds antigenic sites in proteins
digest Reports on protein proteolytic enzyme or reagent cleavage sites
echlorop Reports presence of chloroplast transit peptides
eiprscan Motif detection
elipop Prediction of lipoproteins
emast Motif detection
ememe Multiple EM for Motif Elicitation
ememetext Multiple EM for Motif Elicitation. Text file only
enetnglyc Reports N-glycosylation sites in human proteins
enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian proteins
enetphos Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins
epestfind Finds PEST motifs as potential proteolytic cleavage sites
eprop Reports propeptide cleavage sites in proteins
etmhmm Reports transmembrane helices
eyinoyang Reports O-(beta)-GlcNAc attachment sites
fuzzpro Search for patterns in protein sequences
fuzztran Search for patterns in protein sequences (translated)
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
oddcomp Identify proteins with specified sequence word composition
omeme Motif detection
patmatdb Searches protein sequences with a sequence motif
patmatmotifs Scan a protein sequence with motifs from the PROSITE database
pepcoil Predicts coiled coil regions in protein sequences
preg Regular expression search of protein sequence(s)
pscan Scans protein sequence(s) with fingerprints from the PRINTS database
sigcleave Reports on signal cleavage sites in a protein sequence

Author(s)

This program is an EMBOSS wrapper for a program written by the CBS group http://www.cbs.dtu.dk/index.shtml

The original CBS group application must be licensed and installed to use this wrapper.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None