esignalp |
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% esignalp Reports protein signal cleavage sites Input (aligned) protein 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]: |
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Reports protein signal cleavage sites Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqset (Aligned) protein 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) protein sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||||||||
-type | list | Organism type to use |
|
euk | ||||||||||
-method | list | Method to use |
|
nn+hmm | ||||||||||
-format | list | Output format |
|
full | ||||||||||
-gmode | list | Graphics output |
|
none | ||||||||||
-synver | list | Signalp version weights |
|
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 |
>14KD_DAUCA MGSKNSASVALFFTLNILFFALVSSTEKCPDPYKPKPKPTPKPTPTPYPSAGKCPRDALK LGVCADVLNL |
*********************** 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 |
Program name | Description |
---|---|
echlorop | Reports presence of chloroplast transit peptides |
elipop | Prediction of lipoproteins |
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 |
eprop | Reports propeptide cleavage sites in proteins |
etmhmm | Reports transmembrane helices |
eyinoyang | Reports O-(beta)-GlcNAc attachment sites |
sigcleave | Reports on signal cleavage sites in a protein sequence |
siggenlig | Generates ligand-binding signatures from a CON file |
sigscan | Generates hits (DHF file) from a signature search |
tmap | Predict and plot transmembrane segments in protein sequences |
topo | Draws an image of a transmembrane protein |
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.