oracular (3) Bio::Tools::Prediction::Gene.3pm.gz

NAME

       Bio::Tools::Prediction::Gene - a predicted gene structure feature

SYNOPSIS

         #See documentation of methods.

DESCRIPTION

       A feature representing a predicted gene structure. This class actually inherits off
       Bio::SeqFeature::Gene::Transcript and therefore has all that functionality, plus a few methods supporting
       predicted sequence features, like a predicted CDS and a predicted translation.

       Exons held by an instance of this class will usually be instances of Bio::Tools::Prediction::Exon,
       although they do not have to be. Refer to the documentation of the class that produced the instance.

       Normally, you will not want to create an instance of this class yourself.  Instead, classes representing
       the results of gene structure prediction programs will do that.

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Hilmar Lapp

       Email hlapp-at-gmx.net or hilmar.lapp-at-pharma.novartis.com

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 = $gene->predicted_cds();
                  $gene->predicted_cds($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 = $gene->predicted_protein();
                  $gene->predicted_protein($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.