sigcleave
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Function
Report on signal cleavage sites in a protein sequence
Description
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.
Algorithm
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.
Usage
Here is a sample session with sigcleave
% sigcleave
Report 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
Command line arguments
Report on signal cleavage sites in a protein sequence
Version: EMBOSS:6.6.0.0
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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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
Input file format
sigcleave reads one or more protein sequences.
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.
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 Reviewed; 576 AA.
AC P17644; Q0KI18; Q9VC73;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 18-APR-2012, entry version 123.
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:0045211; C:postsynaptic membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004889; F:acetylcholine-activated cation-selective channel activity
; IEA:InterPro.
DR GO; GO:0004872; F:receptor activity; IEA:UniProtKB-KW.
DR Gene3D; G3DSA:2.70.170.10; Neur_chan_lig_bd; 1.
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.
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 2: Evidence at transcript level;
KW Cell junction; Cell membrane; Complete proteome; Disulfide bond;
KW Glycoprotein; Ion transport; Ionic channel; Ligand-gated ion channel;
KW Membrane; Postsynaptic cell membrane; Receptor; Reference proteome;
KW Signal; Synapse; Transmembrane; Transmembrane helix; 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
//
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, 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.
Output files for usage example
File: ach2_drome.sig
########################################
# Program: sigcleave
# Rundate: Mon 15 Jul 2013 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_length: 576
# Reported_sequences: 1
# Reported_hitcount: 9
#---------------------------------------
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
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.
References
1. von Heijne, G. "A new method for predicting signal sequence
cleavage sites" Nucleic Acids Res.: 14:4683 (1986)
2. 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 Find antigenic sites in proteins
epestfind Find PEST motifs as potential proteolytic cleavage sites
fuzzpro Search for patterns in protein sequences
fuzztran Search for patterns in protein sequences (translated)
patmatdb Search 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 Scan protein sequence(s) with fingerprints from the PRINTS
database
tmap Predict and plot transmembrane segments in protein sequences
Author(s)
Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) 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 (c) emboss.open-bio.org) not to the original author.
History
Completed 10th March 1999
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None