debian man page for bio::seqfeature::gene::transcripti

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
   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 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)