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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::StopCodonReadthroughEdit - Object representing a stop codon readthrough edit in a sequence

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";

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.

METHODS

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