03 Feb 2021 05:15:14 UTC
- Distribution: BioPerl
- Module version: 1.7.8
- Source (raw)
- Browse (raw)
- How to Contribute
- Testers (282 / 7 / 0)
- KwaliteeBus factor: 2
- License: perl_5
- Activity24 month
- Download (7.18MB)
- MetaCPAN Explorer
- Subscribe to distribution
- This version
- Latest version++ed by:17 non-PAUSE usersCJFIELDS Christopher Fieldsand 1 contributors
- See individual modules
- and possibly others
- Reverse dependencies
- CPAN Testers List
- Dependency graph
- AUTHOR - Hilmar Lapp
Bio::Tools::Prediction::Exon - A predicted exon feature
# See documentation of methods.
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.
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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.
Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args :
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 :
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 :
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 :