Bio::Tools::Sigcleave(3pm)				User Contributed Perl Documentation				Bio::Tools::Sigcleave(3pm)

NAME

       Bio::Tools::Sigcleave - Bioperl object for sigcleave analysis

SYNOPSIS

   Object Creation
	 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'

   Object Methods & Accessors
	 # 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

       "Sigcleave" was a program distributed as part of the free EGCG add-on to earlier versions of the GCG Sequence Analysis package. A new
       implementation of the algorithm is now part of EMBOSS package.

       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 implemntation 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

       When updating and maintaining a module, it helps to know that people are actually using it. Let us know if you find a bug, think this code
       is useful or have any improvements/features to suggest.

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Chris Dagdigian, dag-at-sonsorol.org  & others

CONTRIBUTORS

       Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

VERSION

       Bio::Tools::Sigcleave, $Id$

COPYRIGHT

       Copyright (c) 1999 Chris Dagdigian & others. All Rights Reserved.  This module is free software; you can redistribute it and/or modify it
       under the same terms as Perl itself.

REFERENCES 
/ SEE ALSO
       von Heijne G.(1986) "A new method for predicting signal sequences cleavage sites."  Nucleic Acids Res. 14, 4683-4690.

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

APPENDIX

       The following documentation describes the various functions contained in this module. Some functions are for internal use and are not meant
       to be called by the user; they are preceded by an underscore ("_").

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

perl v5.14.2							    2012-03-02						Bio::Tools::Sigcleave(3pm)