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sigcleave |
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sigcleave predicts the site of cleavage between a signal sequence and the mature exported protein using the method of von Heijne. It reads one or more protein sequences and writes a standard EMBOSS report with the position, length and score of each predicted signal sequence. Optionally, you may specify the sequence is prokaryotic and this will change the default scoring data file used. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins.
sigcleave uses the method of von Heijne as modified by von Heijne in his later book where treatment of positions -1 and -3 in the matrix is slightly altered (see references). The minimum scoring weight value (-minweight) for the predicted cleavage site is specified. The value of -minweight should be at least 3.5. At this level, the method should correctly identify 95% of signal peptides, and reject 95% of non-signal peptides. The cleavage site should be correctly predicted in 75-80% of cases.
% sigcleave Reports on signal cleavage sites in a protein sequence Input protein sequence(s): tsw:ach2_drome Minimum weight [3.5]: Output report [ach2_drome.sig]: |
Go to the input files for this example
Go to the output files for this example
Reports on signal cleavage sites in a protein sequence
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqall Protein sequence(s) filename and optional
format, or reference (input USA)
-minweight float [3.5] Minimum scoring weight value for the
predicted cleavage site (Number from 0.000
to 100.000)
[-outfile] report [*.sigcleave] Output report file name
(default -rformat motif)
Additional (Optional) qualifiers:
-prokaryote boolean Specifies the sequence is prokaryotic and
changes the default scoring data file name
Advanced (Unprompted) qualifiers: (none)
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
-rformat2 string Report format
-rname2 string Base file name
-rextension2 string File name extension
-rdirectory2 string Output directory
-raccshow2 boolean Show accession number in the report
-rdesshow2 boolean Show description in the report
-rscoreshow2 boolean Show the score in the report
-rstrandshow2 boolean Show the nucleotide strand in the report
-rusashow2 boolean Show the full USA in the report
-rmaxall2 integer Maximum total hits to report
-rmaxseq2 integer Maximum hits to report for one sequence
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
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| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -minweight | float | Minimum scoring weight value for the predicted cleavage site | Number from 0.000 to 100.000 | 3.5 |
| [-outfile] (Parameter 2) |
report | Output report file name | (default -rformat motif) | <*>.sigcleave |
| Additional (Optional) qualifiers | ||||
| -prokaryote | boolean | Specifies the sequence is prokaryotic and changes the default scoring data file name | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqall 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 report qualifiers | ||||
| -rformat2 -rformat_outfile |
string | Report format | Any string | motif |
| -rname2 -rname_outfile |
string | Base file name | Any string | |
| -rextension2 -rextension_outfile |
string | File name extension | Any string | sig |
| -rdirectory2 -rdirectory_outfile |
string | Output directory | Any string | |
| -raccshow2 -raccshow_outfile |
boolean | Show accession number in the report | Boolean value Yes/No | N |
| -rdesshow2 -rdesshow_outfile |
boolean | Show description in the report | Boolean value Yes/No | N |
| -rscoreshow2 -rscoreshow_outfile |
boolean | Show the score in the report | Boolean value Yes/No | Y |
| -rstrandshow2 -rstrandshow_outfile |
boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y |
| -rusashow2 -rusashow_outfile |
boolean | Show the full USA in the report | Boolean value Yes/No | N |
| -rmaxall2 -rmaxall_outfile |
integer | Maximum total hits to report | Any integer value | 0 |
| -rmaxseq2 -rmaxseq_outfile |
integer | Maximum hits to report for one sequence | Any integer value | 0 |
| 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 |
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
ID ACH2_DROME Reviewed; 576 AA.
AC P17644; Q0KI18; Q9VC73;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 15-JUN-2010, entry version 110.
DE RecName: Full=Acetylcholine receptor subunit alpha-like 2;
DE Flags: Precursor;
GN Name=nAcRalpha-96Ab; Synonyms=Acr96Ab, AcrE, sad; ORFNames=CG6844;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC Ephydroidea; Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY, AND
RP DEVELOPMENTAL STAGE.
RC TISSUE=Head;
RX MEDLINE=90353591; PubMed=2117557; DOI=10.1016/0014-5793(90)81170-S;
RA Jonas P., Baumann A., Merz B., Gundelfinger E.D.;
RT "Structure and developmental expression of the D alpha 2 gene encoding
RT a novel nicotinic acetylcholine receptor protein of Drosophila
RT melanogaster.";
RL FEBS Lett. 269:264-268(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX MEDLINE=90360975; PubMed=1697262;
RA Sawruk E., Schloss P., Betz H., Schmitt B.;
RT "Heterogeneity of Drosophila nicotinic acetylcholine receptors: SAD, a
RT novel developmentally regulated alpha-subunit.";
RL EMBO J. 9:2671-2677(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, AND DEVELOPMENTAL
RP STAGE.
RC TISSUE=Head;
RX MEDLINE=90301489; PubMed=2114015; DOI=10.1093/nar/18.12.3640;
RA Baumann A., Jonas P., Gundelfinger E.D.;
RT "Sequence of D alpha 2, a novel alpha-like subunit of Drosophila
RT nicotinic acetylcholine receptors.";
RL Nucleic Acids Res. 18:3640-3640(1990).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX MEDLINE=20196006; PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
RA Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
RA Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
RA Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
[Part of this file has been deleted for brevity]
DR GO; GO:0005515; F:protein binding; IPI:IntAct.
DR GO; GO:0004872; F:receptor activity; IEA:UniProtKB-KW.
DR GO; GO:0006811; P:ion transport; IEA:UniProtKB-KW.
DR InterPro; IPR006202; Neur_chan_lig_bd.
DR InterPro; IPR006201; Neur_channel.
DR InterPro; IPR006029; Neurotrans-gated_channel_TM.
DR InterPro; IPR018000; Neurotransmitter_ion_chnl_CS.
DR InterPro; IPR002394; Nicotinic_acetylcholine_rcpt_N.
DR Gene3D; G3DSA:2.70.170.10; Neur_chan_lig_bd; 1.
DR PANTHER; PTHR18945; Neur_channel; 1.
DR Pfam; PF02931; Neur_chan_LBD; 1.
DR Pfam; PF02932; Neur_chan_memb; 1.
DR PRINTS; PR00254; NICOTINICR.
DR PRINTS; PR00252; NRIONCHANNEL.
DR SUPFAM; SSF90112; Neu_channel_TM; 1.
DR SUPFAM; SSF63712; Neur_chan_LBD; 1.
DR TIGRFAMs; TIGR00860; LIC; 1.
DR PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1.
PE 1: Evidence at protein level;
KW Cell junction; Cell membrane; Complete proteome; Disulfide bond;
KW Glycoprotein; Ion transport; Ionic channel; Membrane;
KW Postsynaptic cell membrane; Receptor; Signal; Synapse; Transmembrane;
KW Transport.
FT SIGNAL 1 21 Probable.
FT CHAIN 22 576 Acetylcholine receptor subunit alpha-like
FT 2.
FT /FTId=PRO_0000000300.
FT TOPO_DOM 22 261 Extracellular (Potential).
FT TRANSMEM 262 285 Helical; (Potential).
FT TRANSMEM 293 311 Helical; (Potential).
FT TRANSMEM 327 346 Helical; (Potential).
FT TOPO_DOM 347 526 Cytoplasmic (Potential).
FT TRANSMEM 527 545 Helical; (Potential).
FT CARBOHYD 65 65 N-linked (GlcNAc...) (Potential).
FT CARBOHYD 254 254 N-linked (GlcNAc...) (Potential).
FT CARBOHYD 570 570 N-linked (GlcNAc...) (Potential).
FT DISULFID 169 183 By similarity.
FT DISULFID 243 244 Associated with receptor activation (By
FT similarity).
SQ SEQUENCE 576 AA; 65506 MW; 97D6A46CADC3F42F CRC64;
MAPGCCTTRP RPIALLAHIW RHCKPLCLLL VLLLLCETVQ ANPDAKRLYD DLLSNYNRLI
RPVSNNTDTV LVKLGLRLSQ LIDLNLKDQI LTTNVWLEHE WQDHKFKWDP SEYGGVTELY
VPSEHIWLPD IVLYNNADGE YVVTTMTKAI LHYTGKVVWT PPAIFKSSCE IDVRYFPFDQ
QTCFMKFGSW TYDGDQIDLK HISQKNDKDN KVEIGIDLRE YYPSVEWDIL GVPAERHEKY
YPCCAEPYPD IFFNITLRRK TLFYTVNLII PCVGISYLSV LVFYLPADSG EKIALCISIL
LSQTMFFLLI SEIIPSTSLA LPLLGKYLLF TMLLVGLSVV ITIIILNIHY RKPSTHKMRP
WIRSFFIKRL PKLLLMRVPK DLLRDLAANK INYGLKFSKT KFGQALMDEM QMNSGGSSPD
SLRRMQGRVG AGGCNGMHVT TATNRFSGLV GALGGGLSTL SGYNGLPSVL SGLDDSLSDV
AARKKYPFEL EKAIHNVMFI QHHMQRQDEF NAEDQDWGFV AMVMDRLFLW LFMIASLVGT
FVILGEAPSL YDDTKAIDVQ LSDVAKQIYN LTEKKN
//
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The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.
By default the output is in 'motif' format.
########################################
# Program: sigcleave
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: sigcleave
# -sequence tsw:ach2_drome
# Report_format: motif
# Report_file: ach2_drome.sig
########################################
#=======================================
#
# Sequence: ACH2_DROME from: 1 to: 576
# HitCount: 9
#
# Reporting scores over 3.50
#
#=======================================
(1) Score 13.739 length 13 at residues 29->41
Sequence: LLVLLLLCETVQA
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29 41
mature_peptide: NPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQIL
(2) Score 12.135 length 13 at residues 26->38
Sequence: LCLLLVLLLLCET
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26 38
mature_peptide: VQANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKD
(3) Score 10.465 length 13 at residues 28->40
Sequence: LLLVLLLLCETVQ
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28 40
mature_peptide: ANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQI
(4) Score 7.360 length 13 at residues 528->540
Sequence: FLWLFMIASLVGT
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528 540
mature_peptide: FVILGEAPSLYDDTKAIDVQLSDVAKQIYNLTEKKN
(5) Score 6.981 length 13 at residues 330->342
Sequence: FTMLLVGLSVVIT
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330 342
mature_peptide: IIILNIHYRKPSTHKMRPWIRSFFIKRLPKLLLMRVPKDLLRDLAANKIN
(6) Score 5.057 length 13 at residues 24->36
Sequence: KPLCLLLVLLLLC
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24 36
mature_peptide: ETVQANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNL
(7) Score 4.026 length 13 at residues 31->43
Sequence: VLLLLCETVQANP
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31 43
mature_peptide: DAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQILTT
(8) Score 3.751 length 13 at residues 527->539
Sequence: LFLWLFMIASLVG
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527 539
mature_peptide: TFVILGEAPSLYDDTKAIDVQLSDVAKQIYNLTEKKN
(9) Score 3.632 length 13 at residues 308->320
Sequence: LLISEIIPSTSLA
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308 320
mature_peptide: LPLLGKYLLFTMLLVGLSVVITIIILNIHYRKPSTHKMRPWIRSFFIKRL
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_length: 576
# Reported_sequences: 1
# Reported_hitcount: 9
#---------------------------------------
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EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
Here is the default file for eukaryotic signals:
# Amino acid counts for 161 Eukaryotic Signal Peptides, # from von Heijne (1986), Nucl. Acids. Res. 14:4683-4690 # # The cleavage site is between +1 and -1 # Sample: 161 aligned sequences # # R -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 +1 +2 Expect # - --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ------ A 16 13 14 15 20 18 18 17 25 15 47 6 80 18 6 14.5 C 3 6 9 7 9 14 6 8 5 6 19 3 9 8 3 4.5 D 0 0 0 0 0 0 0 0 5 3 0 5 0 10 11 8.9 E 0 0 0 1 0 0 0 0 3 7 0 7 0 13 14 10.0 F 13 9 11 11 6 7 18 13 4 5 0 13 0 6 4 5.6 G 4 4 3 6 3 13 3 2 19 34 5 7 39 10 7 12.1 H 0 0 0 0 0 1 1 0 5 0 0 6 0 4 2 3.4 I 15 15 8 6 11 5 4 8 5 1 10 5 0 8 7 7.4 K 0 0 0 1 0 0 1 0 0 4 0 2 0 11 9 11.3 L 71 68 72 79 78 45 64 49 10 23 8 20 1 8 4 12.1 M 0 3 7 4 1 6 2 2 0 0 0 1 0 1 2 2.7 N 0 1 0 1 1 0 0 0 3 3 0 10 0 4 7 7.1 P 2 0 2 0 0 4 1 8 20 14 0 1 3 0 22 7.4 Q 0 0 0 1 0 6 1 0 10 8 0 18 3 19 10 6.3 R 2 0 0 0 0 1 0 0 7 4 0 15 0 12 9 7.6 S 9 3 8 6 13 10 15 16 26 11 23 17 20 15 10 11.4 T 2 10 5 4 5 13 7 7 12 6 17 8 6 3 10 9.7 V 20 25 15 18 13 15 11 27 0 12 32 3 0 8 17 11.1 W 4 3 3 1 1 2 6 3 1 3 0 9 0 2 0 1.8 Y 0 1 4 0 0 1 3 1 1 2 0 5 0 1 7 5.6
Signal peptides mediate translocation across the endoplasmic reticulum (ER) membrane in eukaryotes. In prokaryotes signal peptides mediate translocation across the inner and outer membranes.
sigcleave may predict any number of cleavage sites in a protein sequence but not all of these will be biologically relevant; the prediction algorithm is not perfect. There is no cutoff to eliminate sites because it is down to human expertise to decide what is relevant or not. Although the end of a protein sequence is usually easy to predict from a nucleotide sequence, the same cannot be said for the start which depends on such things as promoters, transcriptional control and splicing. This is why all predicted cleavage sites are reported.
It is often useful to specify to use just the starting region of the input sequence using the in-built qualifier -send. For example, adding -send 50 to the command-line will check only the first 50 residues.
| Program name | Description |
|---|---|
| antigenic | Finds antigenic sites in proteins |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzzpro | Search for patterns in protein sequences |
| fuzztran | Search for patterns in protein sequences (translated) |
| patmatdb | Searches protein sequences with a sequence motif |
| patmatmotifs | Scan a protein sequence with motifs from the PROSITE database |
| preg | Regular expression search of protein sequence(s) |
| pscan | Scans protein sequence(s) with fingerprints from the PRINTS database |
| tmap | Predict and plot transmembrane segments in protein sequences |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Original program "SIGCLEAVE" (EGCG 1989) by
Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.