| Bio::Tools::Prediction::Gene(3pm) | User Contributed Perl Documentation | Bio::Tools::Prediction::Gene(3pm) |
Bio::Tools::Prediction::Gene - a predicted gene structure feature
#See documentation of methods.
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.
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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 = $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.
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.
| 2021-08-15 | perl v5.32.1 |