/ 
bioperl-1.5.2_004-RC
/ Bio::Tools::Prediction::Gene

NAME

Bio::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

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.