Bio::Tools::Prediction::Exon(3pm)			User Contributed Perl Documentation			 Bio::Tools::Prediction::Exon(3pm)

NAME

       Bio::Tools::Prediction::Exon - A predicted exon feature

SYNOPSIS

	 # See documentation of methods.

DESCRIPTION

       A feature representing a predicted exon. This class actually inherits off Bio::SeqFeature::Gene::Exon and therefore has all that
       functionality (also implements Bio::SeqFeatureI), plus a few methods supporting predicted features, like various scores and a significance.
       Even though these were inspired by GenScan results, at least a subset should be generally useable for exon prediction results.

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-at-gmx.net

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 = $exon->predicted_cds();
		  $exon->predicted_cds($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 = $exon->predicted_protein();
		  $exon->predicted_protein($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.

   significance
	Title	: significance
	Usage	: $evalue = $obj->significance();
		  $obj->significance($evalue);
	Function:
	Returns :
	Args	:

   start_signal_score
	Title	: start_signal_score
	Usage	: $sc = $obj->start_signal_score();
		  $obj->start_signal_score($evalue);
	Function: Get/Set a score for the exon start signal (acceptor splice site
		  or initiation signal).
	Returns :
	Args	:

   end_signal_score
	Title	: end_signal_score
	Usage	: $sc = $obj->end_signal_score();
		  $obj->end_signal_score($evalue);
	Function: Get/Set a score for the exon end signal (donor splice site
		  or termination signal).
	Returns :
	Args	:

   coding_signal_score
	Title	: coding_signal_score
	Usage	: $sc = $obj->coding_signal_score();
		  $obj->coding_signal_score($evalue);
	Function: Get/Set a score for the exon coding signal (e.g., coding potential).
	Returns :
	Args	:

perl v5.14.2							    2012-03-02					 Bio::Tools::Prediction::Exon(3pm)