Provided by: libbio-perl-perl_1.6.901-2_all bug

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:

         https://redmine.open-bio.org/projects/bioperl/

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    :