Bio::EnsEMBL::StopCodonReadthroughEdit Class Reference

Inheritance diagram for Bio::EnsEMBL::StopCodonReadthroughEdit:

Public Member Functions
public Bio::EnsEMBL::StopCodonReadthroughEdit	new ()
Public Member Functions inherited from Bio::EnsEMBL::SeqEdit
public Bio::EnsEMBL::SeqEdit	new ()
public Int	start ()
public Int	end ()
public String	alt_seq ()
public Int	length_diff ()
public String	name ()
public String	code ()
public String	description ()
public Bio::EnsEMBL::Attribute	get_Attribute ()
public Reference	apply_edit ()

Detailed Description

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.

Definition at line 33 of file StopCodonReadthroughEdit.pm.

Member Function Documentation

new()

public Bio::EnsEMBL::StopCodonReadthroughEdit Bio::EnsEMBL::StopCodonReadthroughEdit::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

Code:

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The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/StopCodonReadthroughEdit.pm