| esignalp

## Wiki

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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

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.

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