                                  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:6.2.0

   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


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, So/ren 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.

   Although we take every care to ensure that the results of the EMBOSS
   version are identical to those from the original package, we recommend
   that you check your inputs give the same results in both versions
   before publication.

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   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
