EMBOSS: sigcleave

| ## EMBOSS: sigcleave

# Program sigcleave

## Function

Reports protein signal cleavage sites

## Description

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).

## Usage

Here is a sample session with sigcleave.

    % sigcleave
    Reports peptide signal cleavage sites
    Input sequence: sw:ach2_drome
    Output file [ach2_drome.out]:
    Minimum weight [3.5]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
       -minweight          float      Minimum scoring weight value for the
                                      predicted cleavage site
      [-outfile]           report     (no help text) report value

       Optional qualifiers:
       -prokaryote         bool       Specifies the sequence is prokaryotic and
                                      changes the default scoring data file name

       Advanced qualifiers:
       -pval               integer    Specifies the number of columns before the
                                      residue at the cleavage site in the weight
                                      matrix table
       -nval               integer    specifies the number of columns after the
                                      residue at the cleavage site in the weight
                                      matrix table

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

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) | (no help text) report value | Report file |
Optional qualifiers | Allowed values | Default
-prokaryote | Specifies the sequence is prokaryotic and changes the default scoring data file name | Yes/No | No
Advanced qualifiers | Allowed values | Default
-pval | Specifies the number of columns before the residue at the cleavage site in the weight matrix table | Integer from -13 to -1 | -13
-nval | specifies the number of columns after the residue at the cleavage site in the weight matrix table | Integer 1 or more | Pval+15 (2)

## Input file format

The input sequence can be one or more protein sequences.

## 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://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default sigcleave writes a 'motif' report file.

The output from the above example is:

    ########################################
    # Program: sigcleave
    # Rundate: Mon Feb 11 13:50:56 2002
    # 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 3.632 length 13 at residues 308->320
     Sequence: LLISEIIPSTSLA
               |           |
             308           320
     mature_peptide: LPLLGKYLLFTMLLVGLSVVITIIILNIHYRKPSTHKMRPWIRSFFIKRL

    (3) Score 3.751 length 13 at residues 527->539
     Sequence: LFLWLFMIASLVG
               |           |
             527           539
     mature_peptide: TFVILGEAPSLYDDTKAIDVQLSDVAKQIYNLTEKKN

    (4) Score 4.026 length 13 at residues 31->43
     Sequence: VLLLLCETVQANP
               |           |
              31           43
     mature_peptide: DAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQILTT

    (5) Score 5.057 length 13 at residues 24->36
     Sequence: KPLCLLLVLLLLC
               |           |
              24           36
     mature_peptide: ETVQANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNL

    (6) Score 6.981 length 13 at residues 330->342
     Sequence: FTMLLVGLSVVIT
               |           |
             330           342
     mature_peptide: IIILNIHYRKPSTHKMRPWIRSFFIKRLPKLLLMRVPKDLLRDLAANKIN

    (7) Score 7.360 length 13 at residues 528->540
     Sequence: FLWLFMIASLVGT
               |           |
             528           540
     mature_peptide: FVILGEAPSLYDDTKAIDVQLSDVAKQIYNLTEKKN

    (8) Score 10.465 length 13 at residues 28->40
     Sequence: LLLVLLLLCETVQ
               |           |
              28           40
     mature_peptide: ANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKDQI

    (9) Score 12.135 length 13 at residues 26->38
     Sequence: LCLLLVLLLLCET
               |           |
              26           38
     mature_peptide: VQANPDAKRLYDDLLSNYNRLIRPVSNNTDTVLVKLGLRLSQLIDLNLKD

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

## Data files

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.

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

The data file names are:

- Esig.euk Eukaryotic signal data
- Esig.pro Prokaryotic signal data

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. 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
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)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

Original program "SIGCLEAVE" by Peter Rice (EGCG 1989)

## 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