Bio::Tools::Prediction Exon
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Summary
Bio::Tools::Prediction::Exon - A predicted exon feature
Package variables
No package variables defined.
Inherit
Bio::SeqFeature::Gene::Exon
Synopsis
  # See documentation of methods.
Description
A feature representing a predicted exon. This class actually inherits
off Bio::SeqFeature::Gene::Exon and therefore has all that
functionality (also implements Bio::SeqFeatureI), plus a few methods
supporting predicted features, like various scores and a
significance. Even though these were inspired by GenScan results, at
least a subset should be generally useable for exon prediction
results.
Methods
new
No description
Code
predicted_cdsDescriptionCode
predicted_proteinDescriptionCode
significanceDescriptionCode
start_signal_scoreDescriptionCode
end_signal_scoreDescriptionCode
coding_signal_scoreDescriptionCode
Methods description
predicted_cdscode    nextTop
 Title   : predicted_cds
Usage : $predicted_cds_dna = $exon->predicted_cds();
$exon->predicted_cds($predicted_cds_dna);
Function: Get/Set the CDS (coding sequence) as predicted by a program.
This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. Example : Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. Args : On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program.
predicted_proteincodeprevnextTop
 Title   : predicted_protein
Usage : $predicted_protein_seq = $exon->predicted_protein();
$exon->predicted_protein($predicted_protein_seq);
Function: Get/Set the protein translation as predicted by a program.
This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. Example : Returns : A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. Args : On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program.
significancecodeprevnextTop
 Title   : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args :
start_signal_scorecodeprevnextTop
 Title   : start_signal_score
Usage : $sc = $obj->start_signal_score();
$obj->start_signal_score($evalue);
Function: Get/Set a score for the exon start signal (acceptor splice site
or initiation signal).
Returns :
Args :
end_signal_scorecodeprevnextTop
 Title   : end_signal_score
Usage : $sc = $obj->end_signal_score();
$obj->end_signal_score($evalue);
Function: Get/Set a score for the exon end signal (donor splice site
or termination signal).
Returns :
Args :
coding_signal_scorecodeprevnextTop
 Title   : coding_signal_score
Usage : $sc = $obj->coding_signal_score();
$obj->coding_signal_score($evalue);
Function: Get/Set a score for the exon coding signal (e.g., coding potential).
Returns :
Args :
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    
    my $self = $class->SUPER::new(@args);

    return $self;
}
predicted_cdsdescriptionprevnextTop
sub predicted_cds {
    my ($self, $cds) = @_;

    if(defined($cds)) {
	$self->{'_predicted_cds'} = $cds;
    }
    return $self->{'_predicted_cds'};
}
predicted_proteindescriptionprevnextTop
sub predicted_protein {
    my ($self, $aa) = @_;

    if(defined($aa)) {
	$self->{'_predicted_aa'} = $aa;
    }
    return $self->{'_predicted_aa'};
}
significancedescriptionprevnextTop
sub significance {
    return shift->_tag_value('signif', @_);
}
start_signal_scoredescriptionprevnextTop
sub start_signal_score {
    return shift->_tag_value('AccScore', @_);
}
end_signal_scoredescriptionprevnextTop
sub end_signal_score {
    return shift->_tag_value('DonScore', @_);
}
coding_signal_scoredescriptionprevnextTop
sub coding_signal_score {
    return shift->_tag_value('CodScore', @_);
}

#
# Everything else is just inherited from SeqFeature::Generic.
#
1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 BugsTop
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 - Hilmar LappTop
Email hlapp-at-gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _