bio::tools::prediction::gene(3pm) [debian man page]
Bio::Tools::Prediction::Gene(3pm) User Contributed Perl Documentation Bio::Tools::Prediction::Gene(3pm) 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 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 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 v5.14.2 2012-03-02 Bio::Tools::Prediction::Gene(3pm)
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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)