sigcleave



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Function

   Reports 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
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

Command line arguments

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


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   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
//

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: 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
           |           |
          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        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

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