bio::seqfeature::gene::utr(3pm) [debian man page]

Bio::SeqFeature::Gene::UTR(3pm) 			User Contributed Perl Documentation			   Bio::SeqFeature::Gene::UTR(3pm)

NAME

       Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region
		 that is part of a transcriptional unit

SYNOPSIS

       See documentation of methods

DESCRIPTION

       A UTR is a Bio::SeqFeature::Gene::ExonI compliant object that is non-coding, and can be either 5' or 3' in 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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - David Block
       Email dblock@gene.pbi.nrc.ca

CONTRIBUTORS

       This is based on the Gene Structure scaffolding erected by Hilmar Lapp (hlapp@gmx.net).

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	:
	Function: We override the constructor here to set is_coding to false
		  unless explicitly overridden.

	Example :
	Returns :
	Args	:

   primary_tag
	Title	: primary_tag
	Usage	: $tag = $feat->primary_tag()
	Function: Returns the primary tag for a feature,
		  eg 'utr5prime'.  This method insures that 5prime/3prime information
		  is uniformly stored
	Returns : a string
	Args	: none

perl v5.14.2							    2012-03-02					   Bio::SeqFeature::Gene::UTR(3pm)

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)