/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::SeqFeature::Gene::TranscriptI

NAME

FAST::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

Mailing Lists

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
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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://redmine.open-bio.org/projects/bioperl/

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 FAST::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 FAST::Bio::SeqFeature::Gene::ExonI for properties of the
          returned objects.

Returns : An array of FAST::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 FAST::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 FAST::Bio::SeqFeatureI implementing object.
Args    :

utrs

Title   : utrs()
Usage   : @utr_sites = $transcript->utrs();
Function: Get the UTR regions this transcript comprises of.

          See FAST::Bio::SeqFeature::Gene::ExonI for properties of the
          returned objects.

Returns : An array of FAST::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 FAST::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 FAST::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 FAST::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 FAST::Bio::SeqFeature::Gene::GeneStructureI-compliant object
Args    : a FAST::Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)