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Bio::Tools::Prediction::Exon.3pm

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.

FEEDBACK

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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

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 - 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    :