NAME

       Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a
                transcript of exons, promoter(s), UTR, and a poly-adenylation site.

SYNOPSIS

         #documentation needed

DESCRIPTION

       A feature representing a transcript.

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       of the problem with code and data examples if at all possible.

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AUTHOR - Hilmar Lapp

       Email hlapp@gmx.net

APPENDIX

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

   promoters
        Title   : promoters()
        Usage   : @proms = $transcript->promoters();
        Function: Get the promoter features of this transcript.

                  Note that OO-modeling of regulatory elements is not stable yet.
                  This means that this method might change or even disappear in a
                  future release. Be aware of this if you use it.

        Returns : An array of Bio::SeqFeatureI implementing objects representing the
                  promoter regions or sites.
        Args    :

   exons
        Title   : exons()
        Usage   : @exons = $transcript->exons();
                  @inital = $transcript->exons('Initial');
        Function: Get the individual exons this transcript comprises of, or all exons
                  of a specified type.

                  Refer to the documentation of the class that produced this
                  transcript object for information about the possible types.

                  See Bio::SeqFeature::Gene::ExonI for properties of the
                  returned objects.

        Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
        Args    : An optional string specifying the type of the exon.

   introns
        Title   : introns()
        Usage   : @introns = $transcript->introns();
        Function: Get all introns this transcript comprises of.
        Returns : An array of Bio::SeqFeatureI implementing objects representing the
                  introns.
        Args    :

   poly_A_site
        Title   : poly_A_site()
        Usage   : $polyAsite = $transcript->poly_A_site();
        Function: Get the poly-adenylation site of this transcript.
        Returns : A Bio::SeqFeatureI implementing object.
        Args    :

   utrs
        Title   : utrs()
        Usage   : @utr_sites = $transcript->utrs();
        Function: Get the UTR regions this transcript comprises of.

                  See Bio::SeqFeature::Gene::ExonI for properties of the
                  returned objects.

        Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
        Args    :

   mrna
        Title   : mrna()
        Usage   : $mrna = $transcript->mrna();
        Function: Get the mRNA of the transcript as a sequence object.

        Returns : A Bio::PrimarySeqI implementing object.
        Args    :

   cds
        Title   : cds()
        Usage   : $cds = $transcript->cds();
        Function: Get the CDS (coding sequence) of the transcript as a sequence
                  object.

        Returns : A Bio::PrimarySeqI implementing object.
        Args    :

   protein
        Title   : protein()
        Usage   : $protein = $transcript->protein();
        Function: Get the protein encoded by the transcript as a sequence object.

        Returns : A Bio::PrimarySeqI implementing object.
        Args    :

   parent
        Title   : parent
        Usage   : $obj->parent($newval)
        Function: get the parent gene of the transcript
        Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
        Args    : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)