Lincoln D. Stein


Bio::Das::Segment::GappedAlignment - A Gapped Aligment


  use Bio::Das;

  # contact a DAS server using the "elegans" data source
  my $das      = Bio::Das->new('' => 'elegans');

  # fetch a segment
  my $segment  = $das->segment(-ref=>'CHROMOSOME_I',-start=>10_000,-stop=>20_000);

  # get the alignments
  my @alignments = $segment->features(-category=>'similarity');

  # get the segments from the first alignment
  my @segments = $alignments[0]->segments;

  # get the merged segments from the first alignment
  my @merged = $alignments[0]->merged_segments;

  # get segments the seqFeatureI way:
  my @segments = $alignments[0]->sub_seqFeature;


A Bio::Das::Segment::GappedAlignment is a subclass of Bio::Das::Segment::Feature that is specialized for representing interrupted alignments. It inherits all the methods of its parent class, and adds methods for retrieving the individual aligned regions.


Bio::Das::Segment::GappedAlignment objects are created by calling the features() method of a Bio::Das::Segment object created earlier. See Bio::Das::Segment for details.


All Bio::Das::Segment::Feature methods are available. In particular, the start() and stop() methods will return the start and end of the most proximal and distal aligned segments. The target() method works in the same way.

In addition, this class adds or implements the following methods:

@segments = $feature->segments

The segments() method returns the aligned segments. Each segment is a Bio::Das::Segment::Feature object of category "similarity" (or "homology" for compatibility with earlier versions of the spec). The segments are returned exactly as they were presented by the DAS server, and in the same order.

@segments = $feature->merged_segments

This method works like segments() but adjusts the boundaries of the segments so that overlapping segments are merged into single

@segments = $feature->sub_seqFeature

This is an alias for segments(), and is compatible with the Bio::SeqFeatureI interface.


Lincoln Stein <>.

Copyright (c) 2001 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.


Bio::Das, Bio::Das::Type, Bio::Das::Segment, Bio::Das::Transcript, Bio::Das::Segment::Feature, Bio::RangeI