sigcleave

Function

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

Command line arguments


Input file format

sigcleave reads one or more protein sequence USAs.

Output file format

By default sigcleave writes a 'motif' report file.

Data files

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.

Author(s)

Original program "SIGCLEAVE" (EGCG 1989) by

History

Target users

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