Bio::Tools::Sigcleave(User Contributed Perl DocumentatBio::Tools::Sigcleave(3)NAMEBio::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:
http://bugzilla.open-bio.org/
AUTHOR
Chris Dagdigian, dag-at-sonsorol.org & others
CONTRIBUTORS
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
VERSION
Bio::Tools::Sigcleave, $Id: Sigcleave.pm 16123 2009-09-17 12:57:27Z
cjfields $
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 v5.14.1 2011-07-22 Bio::Tools::Sigcleave(3)
