NAME

SYNOPSIS

  use Bio::Tools::Sigcleave ();

  # to keep the module backwar compatible, you can pass it a sequence string, but
  # there recommended say is to pass it a Seq object

  # this works
  $seq = "MVLLLILSVLLLKEDVRGSAQSSERRVVAHMPGDIIIGALFSVHHQPTVDKVHERKCGAVREQYGI";
  $sig = Bio::Tools::Sigcleave->new(-seq  => $seq,
                                                -type => 'protein',
                                                -threshold=>'3.5',
                                                );
  # but you do:
  $seqobj = Bio::PrimarySeq->new(-seq => $seq);

  $sig = Bio::Tools::Sigcleave->new(-seq  => $seqobj,
                                                -threshold=>'3.5',
                                                );

  # now you can detect procaryotic signal sequences as well as eucaryotic
  $sig->matrix('eucaryotic'); # or 'procaryotic'

  # you can use this method to fine tune the threshod before printing out the results
  $sig->result_count:

  %raw_results      = $sig->signals;
  $formatted_output = $sig->pretty_print;

DESCRIPTION

From the EGCG documentation:

  SigCleave uses the von Heijne method to locate signal sequences, and
  to identify the cleavage site. The method is 95% accurate in
  resolving signal sequences from non-signal sequences with a cutoff
  score of 3.5, and 75-80% accurate in identifying the cleavage
  site. The program reports all hits above a minimum value.

The EGCG Sigcleave program was written by Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SA, UK).

Since EGCG is no longer distributed for the latest versions of GCG, this code was developed to emulate the output of the original program as much as possible for those who lost access to sigcleave when upgrading to newer versions of GCG.

There are 2 accessor methods for this object. "signals" will return a perl associative array containing the sigcleave scores keyed by amino acid position. "pretty_print" returns a formatted string similar to the output of the original sigcleave utility.

In both cases, the "threshold" setting controls the score reporting level. If no value for threshold is passed in by the user, the code defaults to a reporting value of 3.5.

In this implementation the accessor will never return any score/position pair which does not meet the threshold limit. This is the slightly different from the behaviour of the 8.1 EGCG sigcleave program which will report the highest of the under-threshold results if nothing else is found.

Example of pretty_print output:

        SIGCLEAVE of sigtest from: 1 to 146

        Report scores over 3.5
        Maximum score 4.9 at residue 131

         Sequence:  FVILAAMSIQGSA-NLQTQWKSTASLALET
                    | (signal)    | (mature peptide)
                118            131

         Other entries above 3.5

        Maximum score 3.7 at residue 112

         Sequence:  CSRQLFGWLFCKV-HPGAIVFVILAAMSIQGSANLQTQWKSTASLALET
                   | (signal)    | (mature peptide)
                99            112

FEEDBACK

  https://github.com/bioperl/bioperl-live/issues

AUTHOR

CONTRIBUTORS

VERSION

COPYRIGHT

REFERENCES / SEE ALSO

von Heijne G. (1987) in "Sequence Analysis in Molecular Biology: Treasure Trove or Trivial Pursuit" (Acad. Press, (1987), 113-117).

APPENDIX

threshold

 Title     : threshold
 Usage     : $value = $self->threshold
 Purpose   : Read/write method sigcleave score reporting threshold.
 Returns   : float.
 Argument  : new value, float
 Throws    : on non-number argument
 Comments  : defaults to 3.5
 See Also   : n/a

matrix

 Title     : matrix
 Usage     : $value = $self->matrix('procaryotic')
 Purpose   : Read/write method sigcleave matrix.
 Returns   : float.
 Argument  : new value: 'eucaryotic' or 'procaryotic'
 Throws    : on non-number argument
 Comments  : defaults to 3.5
 See Also   : n/a

seq

 Title     : seq
 Usage     : $value = $self->seq($seq_object)
 Purpose   : set the Seq object to be used
 Returns   : Seq object
 Argument  : protein sequence or Seq object
 See Also   : n/a

_Analyze

 Title     : _Analyze
 Usage     : N/A This is an internal method. Not meant to be called from outside
           : the package
           :
 Purpose   : calculates sigcleave score and amino acid position for the
           : given protein sequence. The score reporting threshold can
           : be adjusted by passing in the "threshold" parameter during
           : object construction. If no threshold is passed in, the code
           : defaults to reporting any scores equal to or above 3.5
           :
 Returns   : nothing. results are added to the object
 Argument  : none.
 Throws    : nothing.
 Comments  : nothing.
See Also   : n/a

signals

 Title     : signals
 Usage     : %sigcleave_results = $sig->signals;
           :
 Purpose   : Accessor method for sigcleave results
           : 
 Returns   : Associative array. The key value represents the amino acid position
           : and the value represents the score. Only scores that
           : are greater than or equal to the THRESHOLD value are reported.
           : 
 Argument  : none.
 Throws    : none.
 Comments  : none.
See Also   : THRESHOLD

result_count

 Title     : result_count
 Usage     : $count = $sig->result_count;
           :
 Purpose   : Accessor method for sigcleave results
           : 
 Returns   : Integer, number of results above the threshold
           : 
 Argument  : none.
 Throws    : none.
 Comments  : none.

See Also : THRESHOLD

pretty_print

 Title     : pretty_print
 Usage     : $output = $sig->pretty_print;
           : print $sig->pretty_print;
           :
 Purpose   : Emulates the output of the EGCG Sigcleave
           : utility.
           : 
 Returns   : A formatted string.
 Argument  : none.
 Throws    : none.
 Comments  : none.
See Also   : n/a