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Bio::SeqFeature::SubSeq(3pm) User Contributed Perl Documentation Bio::SeqFeature::SubSeq(3pm)


Bio::SeqFeature::SubSeq - Feature representing a subsequence


  # SubSeq with implicit sequence
  use Bio::Seq;
  my $template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' );
  $subseq = Bio::SeqFeature::Amplicon->new(
      -start    => 6,
      -end      => 15,
      -template => $template,
  print "Subsequence is: ".$amplicon->seq->seq."\n"; # Should be 'CCCCCGGGGG'
  # SubSeq with explicit sequence
  use Bio::SeqFeature::Subseq;
  my $subseq = Bio::SeqFeature::Amplicon->new( 
      -seq => $seq_object,


Bio::SeqFeature::SubSeq extends Bio::SeqFeature::Generic features to represent a subsequence. When this feature is attached to a template sequence, the sequence of feature is the subsequence of the template at this location. The purpose of this class is to represent a sequence as a feature without having to explicitly store its sequence string.

Of course, you might have reasons to explicitly set a sequence. In that case, note that the length of the sequence is allowed to not match the position of the feature. For example, you can set sequence of length 10 in a SubSeq feature that spans positions 30 to 50 of the template if you so desire.


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Florent Angly <>


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new()
 Usage   : my $subseq = Bio::SeqFeature::SubSeq( -start => 1, -end => 10, -strand => -1);
 Function: Instantiate a new Bio::SeqFeature::SubSeq feature object
 Args    : -seq      , the sequence object or sequence string of the feature (optional)
           -template , attach the feature to the provided parent template sequence or feature (optional).
                       Note that you must specify the feature location to do this.
           -start, -end, -location, -strand and all other L<Bio::SeqFeature::Generic> argument can be used.
 Returns : A Bio::SeqFeature::SubSeq object


 Title   : seq()
 Usage   : my $seq = $subseq->seq();
 Function: Get or set the sequence object of this SubSeq feature. If no sequence
           was provided, but the subseq is attached to a sequence, get the
           corresponding subsequence.
 Returns : A sequence object or undef
 Args    : None.


 Title   : seq()
 Usage   : my $length = $subseq->seq();
 Function: Get the length of the SubSeq feature. It is similar to the length()
           method of L<Bio::Generic::SeqFeature>, which computes length based
           on the location of the feature. However, if the feature was not
           given a location, return the length of the subsequence if possible.
 Returns : integer or undef
 Args    : None.
2021-08-15 perl v5.32.1