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sigcleave |
Function
Reports protein signal cleavage sitesDescription
Signal peptides mediate translocation across the ER membrane in eukaryotes. In prokaryotes signal peptides mediate translocation across the inner and outer membranes.sigcleave predicts the site of cleavage between a signal sequence and the mature exported protein. 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).
Why isn't there a cutoff to eliminate internal sites?
The program predicts cleavage sites inside the whole protein. Apart from the N-terminal sites, the other sites are not biologically relevant. Why isn't there a cutoff to eliminate internal sites?The answer is partly because these sites can be relevant in some biological cases (additional pre-processing for example), but mostly because ...
There is one thing in bioinformatics you can not be certain of ... the start of a protein sequence. The end is easy to predict. The start depends on promoters, transcriptional controls, splicing, etc.
Most importantly, sigcleave is not perfect - you should check the results and decide whether you like the prediction.
Also, remember you can put -send 50 on the command line to make sure it only checks the first 50 residues.
Usage
Here is a sample session with sigcleave
% sigcleave Reports protein signal cleavage sites Input 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
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence database USA
-minweight float Minimum scoring weight value for the
predicted cleavage site
[-outfile] report Output report file name
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
-rusashow2 boolean Show the full USA in the report
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write 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. 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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| -minweight | Minimum scoring weight value for the predicted cleavage site | Number from 0.000 to 100.000 | 3.5 |
| [-outfile] (Parameter 2) |
Output report file name | Report output file | |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -prokaryote | Specifies the sequence is prokaryotic and changes the default scoring data file name | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
Input file format
sigcleave reads one or more protein sequence USAs.Input files for usage example
'tsw:ach2_drome' is a sequence entry in the example protein database 'tsw'
Database entry: tsw:ach2_drome
ID ACH2_DROME STANDARD; PRT; 576 AA.
AC P17644;
DT 01-AUG-1990 (REL. 15, CREATED)
DT 01-AUG-1990 (REL. 15, LAST SEQUENCE UPDATE)
DT 01-NOV-1997 (REL. 35, LAST ANNOTATION UPDATE)
DE ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-LIKE CHAIN 2 PRECURSOR.
GN ACRE OR SAD OR ACR96AB.
OS DROSOPHILA MELANOGASTER (FRUIT FLY).
OC EUKARYOTA; METAZOA; ARTHROPODA; TRACHEATA; HEXAPODA; INSECTA;
OC PTERYGOTA; DIPTERA; BRACHYCERA; MUSCOMORPHA; EPHYDROIDEA;
OC DROSOPHILIDAE; DROSOPHILA.
RN [1]
RP SEQUENCE FROM N.A.
RC TISSUE=HEAD;
RX MEDLINE; 90301489.
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 [2]
RP SEQUENCE FROM N.A.
RC TISSUE=HEAD;
RX MEDLINE; 90353591.
RA JONAS P., BAUMANN A., MERZ B., GUNDELFINGER E.D.;
RT "Structure and developmental expression of the D alpha 2 gene
RT encoding a novel nicotinic acetylcholine receptor protein of
RT Drosophila melanogaster.";
RL FEBS LETT. 269:264-268(1990).
RN [3]
RP SEQUENCE FROM N.A.
RX MEDLINE; 90360975.
RA SAWRUK E., SCHLOSS P., BETZ H., SCHMITT B.;
RT "Heterogeneity of Drosophila nicotinic acetylcholine receptors: SAD,
RT a novel developmentally regulated alpha-subunit.";
RL EMBO J. 9:2671-2677(1990).
CC -!- FUNCTION: AFTER BINDING ACETYLCHOLINE, THE ACHR RESPONDS BY AN
CC EXTENSIVE CHANGE IN CONFORMATION THAT AFFECTS ALL SUBUNITS AND
CC LEADS TO OPENING OF AN ION-CONDUCTING CHANNEL ACROSS THE PLASMA
CC MEMBRANE.
CC -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN.
CC -!- TISSUE SPECIFICITY: CNS IN EMBRYOS.
CC -!- DEVELOPMENTAL STAGE: LATE EMBRYONIC AND LATE PUPAL STAGES.
CC -!- SIMILARITY: BELONGS TO THE LIGAND-GATED IONIC CHANNELS FAMILY.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to license@isb-sib.ch).
CC --------------------------------------------------------------------------
DR EMBL; X52274; G7803; -.
DR EMBL; X53583; G8533; -.
DR PIR; S11679; ACFFA2.
DR FLYBASE; FBgn0000039; nAcR-alpha-96Ab.
DR PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1.
DR PFAM; PF00065; neur_chan; 1.
KW RECEPTOR; POSTSYNAPTIC MEMBRANE; IONIC CHANNEL; GLYCOPROTEIN; SIGNAL;
KW TRANSMEMBRANE; MULTIGENE FAMILY.
FT SIGNAL 1 41 PROBABLE.
FT CHAIN 42 576 ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2.
FT DOMAIN 42 261 EXTRACELLULAR (POTENTIAL).
FT TRANSMEM 262 285 POTENTIAL.
FT TRANSMEM 293 311 POTENTIAL.
FT TRANSMEM 327 346 POTENTIAL.
FT DOMAIN 347 526 CYTOPLASMIC (POTENTIAL).
FT TRANSMEM 527 545 POTENTIAL.
FT DISULFID 169 183 BY SIMILARITY.
FT DISULFID 243 244 ASSOCIATED WITH RECEPTOR ACTIVATION
FT (BY SIMILARITY).
FT CARBOHYD 65 65 POTENTIAL.
FT CARBOHYD 254 254 POTENTIAL.
FT CARBOHYD 570 570 POTENTIAL.
SQ SEQUENCE 576 AA; 65506 MW; 7B795689 CRC32;
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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Output file format
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, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq
See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.
By default sigcleave writes a 'motif' report file.
Output files for usage example
File: ach2_drome.sig
########################################
# Program: sigcleave
# Rundate: Fri Jul 15 2005 12:00:00
# 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
#---------------------------------------
#---------------------------------------
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Data files
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:
- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata
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
Notes
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.If you use matrix tables with a different number of residues before or after the cleavage site, you must also set the advanced parameters nval and pval.
References
- von Heijne, G. "A new method for predicting signal sequence cleavage sites" Nucleic Acids Res.: 14:4683 (1986)
- von Heijne, G. "Sequence Analysis in Molecular Biology: Treasure Trove or Trivial Pursuit" (Acad. Press, (1987), 113-117)
Warnings
The program will warn you if a nucleic acid sequence is given or if the data file is not mathematically accurate.Diagnostic Error Messages
Exit status
It exits with status 0 unless an error is reported.Known bugs
None.See also
| Program name | Description |
|---|---|
| antigenic | Finds antigenic sites in proteins |
| digest | Protein proteolytic enzyme or reagent cleavage digest |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzzpro | Protein pattern search |
| fuzztran | Protein pattern search after translation |
| helixturnhelix | Report nucleic acid binding motifs |
| oddcomp | Find protein sequence regions with a biased composition |
| patmatdb | Search a protein sequence with a motif |
| patmatmotifs | Search a PROSITE motif database with a protein sequence |
| pepcoil | Predicts coiled coil regions |
| preg | Regular expression search of a protein sequence |
| pscan | Scans proteins using PRINTS |
Author(s)
Alan Bleasby (ajb © ebi.ac.uk)European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Original program "SIGCLEAVE" (EGCG 1989) by
Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK