05-05-2011
Use objects (struct, array) of integers, implementing carry operations in software rather than in hardware.
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LEARN ABOUT DEBIAN
bio::seqfeature::gene::transcripti
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)