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.

FEEDBACK

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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
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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:

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

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)