/ 
bioperl-1.2.3
/ Bio::SeqFeature::Gene::TranscriptI

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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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)