Christopher Fields > BioPerl-1.6.922 > Bio::SeqFeature::Gene::GeneStructureI

Download:
BioPerl-1.6.922.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  10
Open  4
View/Report Bugs
Module Version: 1.006922   Source   Latest Release: BioPerl-1.6.924

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    : 
syntax highlighting: