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     Output report file name

   Optional qualifiers:
   -prokaryote         boolean    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                boolean    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)
Output report file name 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:

The data file names are: 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 nameDescription
antigenicFinds antigenic sites in proteins
digestProtein proteolytic enzyme or reagent cleavage digest
fuzzproProtein pattern search
fuzztranProtein pattern search after translation
helixturnhelixReport nucleic acid binding motifs
oddcompFinds protein sequence regions with a biased composition
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pepcoilPredicts coiled coil regions
pregRegular expression search of a protein sequence
pscanScans 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