Ewan Birney

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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AUTHOR - Hilmar Lapp

Email hlapp@gmx.net

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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)