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

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

NAME

       Bio::SeqFeature::Gene::GeneStructureI - A feature representing an arbitrarily
		  complex structure of a gene

SYNOPSIS

	 #documentation needed

DESCRIPTION

       A feature representing a gene structure.

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 _

   transcripts
	Title	: transcripts()
	Usage	: @transcripts = $gene->transcripts();
	Function: Get the transcript features/sites of this gene structure.

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

	Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects
		  representing the promoter regions or sites.
	Args	:

   promoters
	Title	: promoters()
	Usage	: @prom_sites = $gene->promoters();
	Function: Get the promoter features/sites of this gene structure.

		  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 = $gene->exons();
		  @inital = $gene->exons('Initial');
	Function: Get all exon features or all exons of specified type of this gene
		  structure.

		  Refer to the documentation of the class that produced this gene
		  structure 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
		  representing the exon regions.
	Args	: An optional string specifying the type of the exon.

   introns
	Title	: introns()
	Usage	: @introns = $gene->introns();
	Function: Get all introns of this gene structure.
	Returns : An array of Bio::SeqFeatureI implementing objects representing the
		  introns.
	Args	:

   poly_A_sites
	Title	: poly_A_sites()
	Usage	: @polyAsites = $gene->poly_A_sites();
	Function: Get the poly-adenylation features/sites of this gene structure.
	Returns : An array of Bio::SeqFeatureI implementing objects representing the
		  poly-adenylation regions or sites.
	Args	:

   utrs
	Title	: utrs()
	Usage	: @utr_sites = $gene->utrs();
	Function: Get the UTR features/sites of this gene structure.

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

	Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
		  representing the UTR regions or sites.
	Args	:

perl v5.14.2							    2012-03-02				Bio::SeqFeature::Gene::GeneStructureI(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)