
                                 sigcleave 



Function

   Reports protein signal cleavage sites

Description

   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


   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
//

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: Thu Jul 15 2004 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
           |           |
          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


#---------------------------------------
#---------------------------------------

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

    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
   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        Finds 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 (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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

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
