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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

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:

   http://bugzilla.open-bio.org/
 
 

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)