=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
Bio::EnsEMBL::StopCodonReadthroughEdit - Object representing a stop codon readthrough edit in a sequence
=head1 SYNOPSIS
use Bio::EnsEMBL::StopCodonReadthroughEdit;
# Get transcript
my $transcript_adaptor = $db->get_TranscriptAdaptor();
my $transcript = $transcript_adaptor->fetch_by_stable_id("ENST00000217347");
$transcript->edits_enabled(1);
print "Before modifiction: $transcript->translate->seq()\n";
# Construct a stop codon readthrough edit object
my $stop_codon_readthrough_edit = Bio::EnsEMBL::StopCodonReadthroughEdit->new(265);
# Apply post translation edit
$transcript->translation->add_Attributes($stop_codon_readthrough_edit->get_Attribute());
my $translated_sequence = $transcript->translate->seq();
print "After modifiction: $translated_sequence\n";
=head1 DESCRIPTION
Biologically, STOP codon readthrough is a rare phenomenon whereby translation
does not terminate at an in-frame STOP codon, but instead continues further downstream.
It is believed the STOP codon is instead read as a 'sense' codon, i.e. encodes for an amino acid.
The location of a STOP codon readthrough is indicated by an asterisk (*) in the post translation sequence.
This class edits the sequence to replace the asterisk (*) with an 'X' to make it similar to RefSeq representation.
=head1 METHODS
=cut
$Bio::EnsEMBL::StopCodonReadthroughEdit::VERSION = '112.0_56'; # TRIAL
$Bio::EnsEMBL::StopCodonReadthroughEdit::VERSION = '112.056';
use strict;
=head2 new
Arg [-POSITION] :
int - start and end position of the stop codon readthrough edit in the sequence
Example : $stop_codon_rt_edit = Bio::EnsEMBL::StopCodonReadthroughEdit->new($position);
Description: Creates a new stop codon readthrough edit object
Returntype : Bio::EnsEMBL::StopCodonReadthroughEdit
Exceptions : none
Caller : general
Status : Stable
=cut
sub new {
my ($self, $position) = @_;
my $class = ref($self) || $self;
my $stop_codon_rt_edit = $class->SUPER::new(
-START => $position,
-END => $position,
-ALT_SEQ => 'X',
-CODE => '_stop_codon_rt');
return $stop_codon_rt_edit;
}
1;