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|
<HTML>
<HEAD>
<TITLE>
EMBOSS: sigcleave
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
sigcleave
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Reports protein signal cleavage sites
<H2>
Description
</H2>
Signal peptides mediate translocation across the ER membrane in
eukaryotes. In prokaryotes signal peptides mediate translocation across
the inner and outer membranes.
<p>
<b>sigcleave</b> 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.
<p>
<b>sigcleave</b> 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).
<H3>
Why isn't there a cutoff to eliminate internal sites?
</H3>
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?
<p>
The answer is partly because these sites can be relevant in some
biological cases (additional pre-processing for example), but mostly
because ...
<p>
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.
<p>
Most importantly, sigcleave is not perfect - you should check the
results and decide whether you like the prediction.
<p>
Also, remember you can put <b>-send 50</b> on the command line to make
sure it only checks the first 50 residues.
<H2>
Usage
</H2>
<b>Here is a sample session with sigcleave</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>sigcleave </b>
Reports protein signal cleavage sites
Input protein sequence(s): <b>tsw:ach2_drome</b>
Minimum weight [3.5]: <b></b>
Output report [ach2_drome.sig]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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
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
-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 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 dying program messages
</pre>
</td></tr></table>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Protein sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-minweight</td>
<td>Minimum scoring weight value for the predicted cleavage site</td>
<td>Number from 0.000 to 100.000</td>
<td>3.5</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i><*></i>.sigcleave</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-prokaryote</td>
<td>Specifies the sequence is prokaryotic and changes the default scoring data file name</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>sigcleave</b> reads one or more protein sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tsw:ach2_drome' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:ach2_drome</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID ACH2_DROME Reviewed; 576 AA.
AC P17644; Q9VC73;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 03-APR-2007, entry version 78.
DE Acetylcholine receptor subunit alpha-like 2 precursor.
GN Name=nAcR-alpha-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.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
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 [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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 [3]
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 [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.,
RA Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
RA Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
RA Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
<font color=red> [Part of this file has been deleted for brevity]</font>
DR IntAct; P17644; -.
DR Ensembl; CG6844; Drosophila melanogaster.
DR KEGG; dme:Dmel_CG6844; -.
DR FlyBase; FBgn0000039; nAcR-alpha-96Ab.
DR BioCyc; DMEL-XXX-02:DMEL-XXX-02-013190-MONOMER; -.
DR BioCyc; DMEL-XXX-02:DMEL-XXX-02-013191-MONOMER; -.
DR GermOnline; CG6844; Drosophila melanogaster.
DR GO; GO:0005515; F:protein binding; IPI:IntAct.
DR InterPro; IPR006029; Neu_channel_TM.
DR InterPro; IPR006202; Neur_chan_lig_bd.
DR InterPro; IPR006201; Neur_channel.
DR InterPro; IPR002394; Nic_ach_rcpt.
DR Gene3D; G3DSA:3.30.1100.20; Neur_chan_lig_bd; 1.
DR PANTHER; PTHR18945; Neur_channel; 2.
DR Pfam; PF02931; Neur_chan_LBD; 1.
DR Pfam; PF02932; Neur_chan_memb; 1.
DR PRINTS; PR00254; NICOTINICR.
DR PRINTS; PR00252; NRIONCHANNEL.
DR TIGRFAMs; TIGR00860; LIC; 1.
DR PROSITE; PS00236; NEUROTR_ION_CHANNEL; 1.
KW Complete proteome; Glycoprotein; Ion transport; Ionic channel;
KW Membrane; Postsynaptic membrane; Receptor; Signal; 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 Potential.
FT TRANSMEM 293 311 Potential.
FT TRANSMEM 327 346 Potential.
FT TOPO_DOM 347 526 Cytoplasmic (Potential).
FT TRANSMEM 527 545 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
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<p>
The output is a standard EMBOSS report file.
<p>
The results can be output in one of several styles by using the
command-line qualifier <b>-rformat xxx</b>, 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
<p>
See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.
<p>
<p>
By default <b>sigcleave</b> writes a 'motif' report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: ach2_drome.sig</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: sigcleave
# Rundate: Sun 15 Jul 2007 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
| |
29 41
mature_peptide: NPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQIL
(2) Score 12.135 length 13 at residues 26->38
Sequence: LCLLLVLLLLCET
| |
26 38
mature_peptide: VQANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKD
(3) Score 10.465 length 13 at residues 28->40
Sequence: LLLVLLLLCETVQ
| |
28 40
mature_peptide: ANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQI
(4) Score 7.360 length 13 at residues 528->540
Sequence: FLWLFMIASLVGT
| |
528 540
mature_peptide: FVILGEAPSLYDDTKAIDVQLSDVAKQIYNLTEKKN
(5) Score 6.981 length 13 at residues 330->342
Sequence: FTMLLVGLSVVIT
| |
330 342
mature_peptide: IIILNIHYRKPSTHKMRPWIRSFFIKRLPKLLLMRVPKDLLRDLAANKIN
(6) Score 5.057 length 13 at residues 24->36
Sequence: KPLCLLLVLLLLC
| |
24 36
mature_peptide: ETVQANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNL
(7) Score 4.026 length 13 at residues 31->43
Sequence: VLLLLCETVQANP
| |
31 43
mature_peptide: DAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQILTT
(8) Score 3.751 length 13 at residues 527->539
Sequence: LFLWLFMIASLVG
| |
527 539
mature_peptide: TFVILGEAPSLYDDTKAIDVQLSDVAKQIYNLTEKKN
(9) Score 3.632 length 13 at residues 308->320
Sequence: LLISEIIPSTSLA
| |
308 320
mature_peptide: LPLLGKYLLFTMLLVGLSVVITIIILNIHYRKPSTHKMRPWIRSFFIKRL
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 9
#---------------------------------------
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
<p>
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.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
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".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<p>
Here is the default file for eukaryotic signals:
<p>
<pre>
# 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
</pre>
<H2>
Notes
</H2>
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.
<p>
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.
<H2>
References
</H2>
<ol>
<li> von Heijne, G. "A new method for predicting signal sequence
cleavage sites" Nucleic Acids Res.: 14:4683 (1986)
<li>
von Heijne, G. "Sequence Analysis in Molecular Biology: Treasure Trove or
Trivial Pursuit" (Acad. Press, (1987), 113-117)
</ol>
<H2>
Warnings
</H2>
The program will warn you if a nucleic acid sequence is given or if the
data file is not mathematically accurate.
<H2>
Diagnostic Error Messages
</H2>
<H2>
Exit status
</H2>
It exits with status 0 unless an error is reported.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="antigenic.html">antigenic</a></td>
<td>Finds antigenic sites in proteins</td>
</tr>
<tr>
<td><a href="digest.html">digest</a></td>
<td>Protein proteolytic enzyme or reagent cleavage digest</td>
</tr>
<tr>
<td><a href="epestfind.html">epestfind</a></td>
<td>Finds PEST motifs as potential proteolytic cleavage sites</td>
</tr>
<tr>
<td><a href="fuzzpro.html">fuzzpro</a></td>
<td>Protein pattern search</td>
</tr>
<tr>
<td><a href="fuzztran.html">fuzztran</a></td>
<td>Protein pattern search after translation</td>
</tr>
<tr>
<td><a href="helixturnhelix.html">helixturnhelix</a></td>
<td>Report nucleic acid binding motifs</td>
</tr>
<tr>
<td><a href="oddcomp.html">oddcomp</a></td>
<td>Find protein sequence regions with a biased composition</td>
</tr>
<tr>
<td><a href="patmatdb.html">patmatdb</a></td>
<td>Search a protein sequence with a motif</td>
</tr>
<tr>
<td><a href="patmatmotifs.html">patmatmotifs</a></td>
<td>Search a PROSITE motif database with a protein sequence</td>
</tr>
<tr>
<td><a href="pepcoil.html">pepcoil</a></td>
<td>Predicts coiled coil regions</td>
</tr>
<tr>
<td><a href="preg.html">preg</a></td>
<td>Regular expression search of a protein sequence</td>
</tr>
<tr>
<td><a href="pscan.html">pscan</a></td>
<td>Scans proteins using PRINTS</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<p>
Original program "SIGCLEAVE" (EGCG 1989) by
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Completed 10th March 1999
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
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