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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Prediction::Exon 3pm"
.TH Bio::Tools::Prediction::Exon 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Tools::Prediction::Exon \- A predicted exon feature
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # See documentation of methods.
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "Mailing Lists"
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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Hilmar Lapp"
.IX Header "AUTHOR - Hilmar Lapp"
Email hlapp\-at\-gmx.net
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
.SS "predicted_cds"
.IX Subsection "predicted_cds"
.Vb 4
\& 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.
.Ve
.SS "predicted_protein"
.IX Subsection "predicted_protein"
.Vb 4
\& 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.
.Ve
.SS "significance"
.IX Subsection "significance"
.Vb 6
\& Title   : significance
\& Usage   : $evalue = $obj\->significance();
\&           $obj\->significance($evalue);
\& Function: 
\& Returns : 
\& Args    :
.Ve
.SS "start_signal_score"
.IX Subsection "start_signal_score"
.Vb 7
\& 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    :
.Ve
.SS "end_signal_score"
.IX Subsection "end_signal_score"
.Vb 7
\& 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    :
.Ve
.SS "coding_signal_score"
.IX Subsection "coding_signal_score"
.Vb 6
\& 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    :
.Ve