Bio::Tools::PredictionUsernContributed Perl DocBio::Tools::Prediction::Gene(3)NAMEBio::Tools::Prediction::Gene - a predicted gene structure feature
SYNOPSIS
#See documentation of methods.
DESCRIPTION
A feature representing a predicted gene structure. This class actually
inherits off Bio::SeqFeature::Gene::Transcript and therefore has all
that functionality, plus a few methods supporting predicted sequence
features, like a predicted CDS and a predicted translation.
Exons held by an instance of this class will usually be instances of
Bio::Tools::Prediction::Exon, although they do not have to be. Refer to
the documentation of the class that produced the instance.
Normally, you will not want to create an instance of this class
yourself. Instead, classes representing the results of gene structure
prediction programs will do that.
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:
http://bugzilla.open-bio.org/
AUTHOR - Hilmar Lapp
Email hlapp-at-gmx.net or hilmar.lapp-at-pharma.novartis.com
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
predicted_cds
Title : predicted_cds
Usage : $predicted_cds_dna = $gene->predicted_cds();
$gene->predicted_cds($predicted_cds_dna);
Function: Get/Set the CDS (coding sequence) as predicted by a program.
This method is independent of an attached_seq. There is no
guarantee whatsoever that the returned CDS has anything to do
(e.g., matches) with the sequence covered by the exons as annotated
through this object.
Example :
Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence
defined as coding by a prediction of a program.
Args : On set, a Bio::PrimarySeqI implementing object holding the DNA
sequence defined as coding by a prediction of a program.
predicted_protein
Title : predicted_protein
Usage : $predicted_protein_seq = $gene->predicted_protein();
$gene->predicted_protein($predicted_protein_seq);
Function: Get/Set the protein translation as predicted by a program.
This method is independent of an attached_seq. There is no
guarantee whatsoever that the returned translation has anything to
do with the sequence covered by the exons as annotated
through this object, or the sequence returned by predicted_cds(),
although it should usually be just the standard translation.
Example :
Returns : A Bio::PrimarySeqI implementing object holding the protein
translation as predicted by a program.
Args : On set, a Bio::PrimarySeqI implementing object holding the protein
translation as predicted by a program.
perl v5.14.1 2011-07-22 Bio::Tools::Prediction::Gene(3)
