Bio::SeqFeature::Gene::TranscriptI(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::TranscriptI(3pm)
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
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)
perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::TranscriptI(3pm)