GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::SEQFEATURE::GENE::TRANSCRIPTI (3)

.ds Aq ’

NAME

Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a
transcript of exons, promoter(s), UTR, and a poly-adenylation site.

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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)



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::SEQFEATURE::GENE::TRANSCRIPTI (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.