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