Bio::Tools::Prediction::Exon(3p)

NAME
Bio::Tools::Prediction::Exon - A predicted exon feature

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.

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  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:

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AUTHOR - Hilmar Lapp
Email hlapp-at-gmx.net

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  predicted_cds
 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_protein
 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.

  significance
 Title   : significance
 Usage   : $evalue = $obj->significance();
           $obj->significance($evalue);
 Function:
 Returns :
 Args    :

  start_signal_score
 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_score
 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_score
 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    :