Provided by: libbio-perl-perl_1.6.901-2_all bug

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