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

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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email hlapp@gmx.net Describe contact details here 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)