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

     http://www.apache.org/licenses/LICENSE-2.0

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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