Bio::Graphics::Browser2::Plugin::Aligner - Dump multiple alignments from GBrowse


In the appropriate gbrowse configuration file:

 plugins = Aligner

 # and later
 alignable_tracks   = EST
 upcase_tracks      = CDS Motifs
 upcase_default     = CDS


The Aligner plugin dumps multiple nucleotide-to-nucleotide alignments in text form. For it to work properly, the genomic DNA must be loaded, as well as the DNAs for each of the aligned objects. In addition, the GFF load file must represent both the source and the target of the alignment using the Target notation. For example:

  ctgA  est  match  1050  3202  .  +  .  Target EST:agt830.5 1 554
  ctgA  est  HSP    1050  1500  .  +  .  Target EST:agt830.5 1 451
  ctgA  est  HSP    3000  3202  .  +  .  Target EST:agt830.5 452 654


The following options are recognized. They must be placed into a configuration file section named [Aligner:plugin].

 Option             Description

 alignable_tracks   Space-delimited list of tracks to include in
                    the multiple alignment. The genome is always
                    included. If this option is not present, then
                    gbrowse will automatically include any track
                    that has the "draw_target" option set.

 upcase_tracks      Space-delimited list of tracks that will be used
                    to UPCASE the genomic DNA. This is very useful if
                    you want to embed the positions of coding regions
                    or other features inside the multiple alignment.
                    Uppercasing will not be turned on by default. The
                    user must press the "Configure" button, and select
                    which of the uppercase tracks are to be activated
                    from a radiolist.
 upcase_default     A space-delimited list of tracks that will be uppercased
                    by default.

 ragged_default     A small integer indicating that the aligner should
                    include some unaligned bases from the end of each sequence.
                    This is useful for seeing the sequencing primer or cloning
                    site in ESTs.


None known yet.




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.