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

NAME

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

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

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

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