/ 
bioperl-0.6
/ Bio::Tools::Sigcleave

NAME

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

SYNOPSIS

Object Creation

use Bio::Tools::Sigcleave ();

$sigcleave_object = new Bio::Tools::Sigcleave(-file=>'sigtest.aa',
                                              -desc=>'test sigcleave protein seq',
                                              -type=>'AMINO',
                                              -threshold=>'3.5',
                                             );

Sigcleave objects can be created via the same methods as Bio::Seq objects. The one additional parameter is "-threshold" which sets the score reporting limit for the algorithim. The above exmple shows a sigcleave object being created from a protein sequence file. See the Bio::Seq documention to see the other ways that objects can be created.

Object Methods & Accessors

%raw_results      = $sigcleave_object->signals;

$formatted_output = $sigcleave_object->pretty_print;

INSTALLATION

This module is included with the central Bioperl distribution:

http://bio.perl.org/Core/Latest
ftp://bio.perl.org/pub/DIST

Follow the installation instructions included in the README file.

DESCRIPTION

"Sigcleave" was a program distributed as part of the free EGCG add-on to earlier versions of the GCG Sequence Analysis 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.

The EGCG website can be found at: http://www.sanger.ac.uk/Software/EGCG/

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

USAGE

No warranty implied or expressed. Use at your own risk :) Users unfamiliar with the original Sigcleave application should read the von Heijne papers.

The emphasis here is on correctly replicating the calls that 8.1 EGCG sigcleave would make. This code has been tested against a non-redundant curated set of 405 Swissprot proteins representing secreted, non-secreted, membrane and transit proteins. Except for the EGCG sigcleave habit of reporting an under-threshold score if nothing better is found the output was identical.

The weight matrix in this code is for eukaryote signal sequences.

Please see the example script located in the bioperl distribution to see how this code can be used.

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.

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 email or the web:

bioperl-bugs@bio.perl.org                   
http://bio.perl.org/bioperl-bugs/

AUTHOR

Chris Dagdigian, dag@sonsorol.org & others

VERSION

Bio::Tools::Sigcleave.pm, $Id: Sigcleave.pm,v 1.9 2000/02/14 13:37:59 birney Exp $

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).

EGCG website: http://www.sanger.ac.uk/Software/EGCG/

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 ("_").

_initialize

Title     : _initialize
Usage     : n/a; automatically called by Bio::Root::Object::new()
Purpose   : Verifies that the type is correct for superclass (Bio::Seq.pm)
          : and calls superclass constructor last.
Returns   : n/a
Argument  : Parameters passed to new()
Throws    : Exception if given type is not protein.
Comments  : 
See Also   : B<Bio::Root::Object::new()>, B<Bio::Seq::_initialize()>

_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

threshold

Title     : threshold
Usage     : $value = $self->threshold 
          :
Purpose   : Accessor method sigcleave score reporting threshold.
          : 
Returns   : float.
          : 
Argument  : none. 
Throws    : none.
Comments  : none.
See Also   : n/a

signals

Title     : signals
Usage     : %sigcleave_results = $sigcleave_object->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

pretty_print

Title     : pretty_print
Usage     : $output = $sigcleave_object->pretty_print;
          : print $sigcleave_object->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